Makoto Naegi

Makoto Naegi (苗木 誠), is a student in Hope's Peak Academy's Class 78th, and a participant of the Killing School Life featured in Danganronpa: Trigger Happy Havoc. His title is the Ultimate Lucky Student (超高校級の「幸運」lit. Super High School Level Good Luck).

Years later, he is a participant of the Final Killing Game featured in Danganronpa 3: The End of Hope's Peak High School with the Future Foundation Directors.

Appearance
At the beginning of the Killing School Life in Danganronpa: Trigger Happy Havoc, Makoto appears to be and believes himself to be a younger teenager, two years of his life having been removed from his memory. He is notably short compared to most of his classmates. He has spiky, desaturated brown hair with a prominent, and washed-out hazel eyes. He wears black jeans, a zipped-up dull green hoodie with a red stripe along the zipper, an open black jacket with gold buttons, and red sneakers with white toes.

Makoto's hoodie has an image of a red gas mask in a circle printed on the back of the hood, and the zipper goes all the way up to the top of the hood. He wears a pin shaped like a four-pointed star overlaying a crescent moon; this is pinned to the lapel of his jacket.

After joining the Future Foundation post-Killing School Life, Makoto is seen wearing a black suit. In Danganronpa: Another Episode, his hair is noticeably lighter, longer, spikier, and overall slightly more detailed. In Danganronpa 3, it appears that Makoto had cut his hair, as it is considerably shorter. He also looks more mature, though still has a bit round face for his adult age. After he becomes the headmaster of the new Hope's Peak Academy, he wears a black suit and a beige tie, as well as a dark blue sweater vest with a white shirt underneath.

Personality
Makoto proclaims himself to be a very ordinary person, to the point that he seems a bit insecure about it. He does admit to having one distinguishing feature, that being his unique sense of optimism.

Makoto is very kind, supportive and forgiving, though slightly naive at times. He is friendly, polite and a lot more down-to-earth compared to the other students. These qualities could be the reason he seems to successfully approach and befriend even his most antisocial classmates during Free Time.

Junko refers to Makoto as an "herbivore man," which means that he is likely to be the passive one in a relationship, which is reinforced in some of his conversations with others. He is a bit jumpy at times and can be somewhat of a pushover. Despite these meeker qualities, he is capable of being a very determined and charismatic speaker.

Makoto is a firm believer in hope, having a positive attitude about the future no matter how bad the situation is in the present. He is also a pacifist, as he tends to believe that violence isn't the answer. While he dislikes despair, believing it to be a corrupting and negative emotion which cannot benefit the world, he is very forgiving toward those who have fallen to despair, believing them to be victims of Junko and not inherently evil.

It appears that the only person Makoto genuinely dislikes is Junko Enoshima, the True Ultimate Despair. He considers her his enemy, and blames Junko as well as her avatar, Monokuma, for the deaths of his friends during the Killing Game. However, even in her case, he felt that death wasn't necessary and tried to reason with her when she was preparing to execute herself. Junko refused to listen and executed herself anyway.

Makoto is respected by many people as the Ultimate Hope, though he himself is very humble and even a bit embarrassed in regards to the title. In Danganronpa Zero, it's mentioned that he has incredible strength inside, despite often appearing weaker on the outside. During hard times, he is shown to have the power to provide hope for other people and ultimately affect their way of thinking, though this is not always the case as some people refuse to listen to him or simply do not accept his ideals.

His title as the Ultimate Hope is but a title, as he is not immune to the effects of the Suicide Video.

Ultimate Lucky Student
Makoto got his talent as the Ultimate Lucky Student by winning a lottery out of completely ordinary students, which led to him joining Hope's Peak Academy as the Ultimate Lucky Student. In addition to this, he was caught up in a bizarre series of events on the day of his selection which ended up catching a jewel thief and burning the selection ticket. Following the fifth trial, just before Makoto's execution can be completed, Alter Ego suddenly appears and is able to prevent Makoto from dying by opening up a door on the floor. He is then rescued by Kyoko, going on to defeat Junko herself and survive the whole ordeal.

Makoto's luck also comes into play during the events of the Final Killing Game, saving him from multiple dangerous situations. While his luck isn't nearly as powerful as his predecessor's or Izuru Kamukura's, his luck pattern is different from those two, and is difficult for Junko to analyze and predict. Thus, Junko predicted that he could possibly ruin her perfect layout plan, which ironically also made Junko allow him to live for the Killing School Life.

Ultimate Hope
Makoto discovers his true talent as the Ultimate Hope during the sixth and final trial of the Killing School Life. Interestingly, unlike most other talents, Makoto being the Ultimate Hope isn't recognized by Hope's Peak Academy, but rather earned for defeating Junko, the True Ultimate Despair. Unlike Izuru Kamukura, who's Ultimate Hope comes from him being the embodiment of talent, Makoto's Ultimate Hope comes from his unusual amount of optimism and determination, which Makoto even comments on.

As the Ultimate Hope, Makoto proves to have an immunity to Junko's tactics, built to make people fall into despair. Combined with his luck being difficult for Junko to analyze, causes her to leave him alive because defying her would be full of despair in its own right. Ultimately, Makoto’s talent aided him in defeating her by filling the other five remaining participants with hope, after they fell into despair over finding out about the state of the world they were in. Makoto is also able to convince others to act with hope simply by spreading his hope to them. When the surviving members of the game are filled with hope, they were persuaded to choose to leave the academy and go out and see what the world had in store for them. In addition, in Danganronpa IF, Makoto unwittingly convinced Mukuro Ikusaba, one of the Despair Sisters, to think of the world outside of Junko's plans to spread despair all over it.

Makoto has even been encouraged by his own hope multiple times, thanks to his friends. After finding out that Kazuo Tengan has been murdered by Kyosuke Munakata, Makoto begins to break down over the fact that he’s been unable to stop people from killing each other. However, Aoi, along with Miaya Gekkogahara (controlled by Monaca Towa), were able to cheer him up, saying that he has given them hope and that they're willing to shoulder his burden. Later, Kyoko tells Makoto that he shouldn't give up on hope, and that she'll always be there for him if his power doesn’t prove to be enough. After her apparent death, Makoto was able to use his and Kyoko's hope in order to convince Kyosuke to join him and combine their hopes together.

Makoto believes that hope is infectious. True to his words, Makoto's effort in defeating Junko, protecting the Remnants of Despair in the Neo World Program, and his firm ideals and optimism eventually become fruitful as he could overcome all despairs at the end of his adventure in Hope's Peak Series.

Keen Intellect
Throughout the series, Makoto has proven to be quite intelligent noticing contradictions in peoples testaments that both Byakuya and Kyoko missed. He was able to decipher Kyosuke's NG code based on the fact he hasn't opened a door since the killing game began. Makoto then went on to use this NG Code to his advantage, setting up a plan to trap Kyosuke so that he can speak with him and subsequently convinced him to join his side.

Prior to the Tragedy
Makoto lived a normal life with his parents and little sister, Komaru. They also had a dog during his childhood. Although sometimes he didn't get along with his sister, he had a close relationship with Komaru. The two watched TV and shared thoughts on manga together.

In a typical day with Makoto and his family, his mother would always watch the same talk show at lunchtime, and his dad wouldn't shave his beard on Saturday when he didn't have work.

In middle school, Makoto went to Blackroot Junior High with Sayaka Maizono, however he was in class 2 while Sayaka was in class 4. He found a lost crane and rescued it; this act of kindness caught her attention, and that was how she remembers him even years later. It's implied that Makoto had a crush on her, but they never talked due to them being in different social standards. Later, he went to Dusk High School.

Makoto had normal school, normal friends, and a normal family. He was pretty much the textbook example of a normal high school student.

Makoto was selected to attend Hope's Peak Academy's Class 78th through winning a random lottery, and on August 20, 2010 (2013 in the anime), Makoto visited a forum and looked up information about his future classmates.

Makoto Naegi Secret File
The day when Makoto was selected to attend Hope's Peak Academy seemed like an ordinary day at first.

Makoto was going home from school and he was in a cheery mood thanks to the clear weather. He had a feeling that something good might happen to him. One thought occurred to him - maybe he should take the long way home. He thought about doing something different than usual.

Makoto passed by a park, and saw a group of his friends trying to decide who to send to the convenience store in a game of rock-paper-scissors. They invited Makoto to join the game, and although Makoto would've usually refused it (he didn't know more than half of the people anyways), he felt that he might as well do something different in this case as well. Plus - there were about 10 people in the group. He didn't think losing was a big possibility. Yet he lost on the first round. Everyone except for him put out rock, while he played scissors. His friends were astonished at just how unlucky Makoto was, but sent him off to the convenience store to buy them snacks and drinks regardless.

Ten minutes later, Makoto was struggling with the two heavy bags filled with the stuff he got from the convenience store. He tried to distract himself by thinking of the music show that'll be on TV tonight - featuring Sayaka Maizono. Yet as his mood began to improve, misfortune struck again. Both of the plastic bags tore open at the same time, spilling their contents all across the pavement. A few minutes passed and Makoto finished collecting all the cans and bags, but wondered for a moment, as he felt like the stuff he managed to gather was less than what he had started out with. He looked around and spotted an old man sitting on the bench. The old man slowly bent down and picked up a can of coffee that rolled to a stop at his feet, opened it up and drank it. That can of coffee belonged to Makoto - yet the old man said he felt that it was natural to drink it since it ended up right in front of him. Makoto was flabbergasted at this incredulous excuse, and revealed to the old man that he seemed to be having a very unlucky day, complaining that he didn't do anything bad enough to deserve this streak of misfortune. The old man laughed and told Makoto that he didn't believe in karma at all. He'd seen plenty of evil people be blessed with fortune, and plenty of kind people suffer all sorts of misfortune. In the end, he says, luck isn't something that a man can control, no matter how much talent one has or how hard one works. He suggests for Makoto to just accept things the way they are.

After finishing their conversation, the old man returned the half-empty can of coffee back to Makoto and left, yet Makoto noticed that the old man had left his phone on the bench. He called out to the old man, who was already a distance away, but the old man seemed deaf to his calls. Makoto was conflicted - should he just ignore the phone and bring the snacks to the park, or should he leave those snacks and chase after the old man? He eventually decided on the latter, and rushed after the old man. His calls were once again drowned out - this time by the sound of a bus coming to a stop ahead. The old man immediately took off towards the bus station - Makoto panicked slightly and upped his own pace as well, and managed to hop into the bus after the old man in the nick of time. Makoto found the old man sitting in the back, and just as he was about to head there, his legs wobbled from the intense running and he lost his balance. Just before he crashed to the ground, he instinctively grabbed onto something. He heard the sound of something tearing and fell to the ground regardless. Makoto's sole consolation was that he managed to soften his fall somewhat by grabbing onto the mysterious object, but even that turned out to be simply a continuation of his misfortune.

Makoto happened to tear open a bag, from which spilled dozens of precious jewelry. The owner of the bag, someone looking like your average salaryman, immediately took out a knife and demanded everyone to freeze. The man was named Jutarō Akafuku. He was a robber who had been blessed with fortune for as long as he was alive. He was just done robbing a small jewelry shop and it all went smoothly, until he was involved in Makoto's misfortune, which could not be overcome even with his unnatural luck. Makoto experienced a minor breakdown thanks to the series of incredibly unlucky events. And to think it all started from him taking a long way home - he couldn't even wrap his head around everything. Correctly identifying Makoto as the cause of his recent misfortune, Jutarō decided to take him hostage and got the driver out of his seat by threatening to slit Makoto's throat if he didn't comply. Jutarō sat Makoto down in the driver's seat and used him as a hostage. In the meanwhile, he ordered the passengers in the bus to gather the scattered pieces of jewelry for him, promising their safety if they cooperated. However, just as someone finished gathering all the pieces, the old man, who had been faking sleep up till that point, sprang up and tackled Jutarō, pinning him on the ground. The old man was a kendo master.

At that precise instant, one thought ran through Makoto's mind particularly strongly - he must save the old man. Makoto feels willing to fight, but that was all for naught as the bus suddenly accelerated - Makoto had accidentally shifted the gears and stepped on the gas pedal. The bus lurched forward, throwing both Makoto and the old man off balance. The old man yelled at Makoto to step on the brakes, which Makoto did immediately, putting the bus to an abrupt stop that knocked him off balance once again. As Makoto was regaining his balance, his hand accidentally brushed over a button. It was a button to open the bus's door. Jutaro saw this as an opportunity and immediately hightailed it out of the bus. The old man was writhing on the ground in pain and shouted at Makoto to chase after the robber. Makoto couldn't believe that he'd ask someone of his stature to chase after a grown man - and capture him, no less. But for some reason, the entire bus seemed to be in agreement. Makoto sought out the bus driver for assistance - surely he would point out how ridiculous this situation was - but found the bus driver passed out.

Left with no choice, Makoto jumped out of the bus, only to crash into a postman who took note of the bus's erratic movements and came over to check. Both of them fell over - Makoto lamenting his bad luck again before noticing Jutarō riding the motorcycle that once belonged to the postman. Jutarō threatened Makoto by saying that he'd hate him for the rest of his life if he ended up being arrested. Jutarō started the engine and accelerated, believing that he could escape successfully. The postman shouted at him, and Makoto simply stood there unmoving. He was tired of the streak of misfortune that seemed to follow him at every step and decided to give up and do nothing. He just wanted to go back to his normal daily life as an ordinary high school student.

At that moment, the motorcycle that Jutarō was riding tipped over and threw the man across the street. The motorcycle spun wildly and hit a streetlamp before exploding in a shower of sparks and smoke, burning up the bag of letters that the postman had put on it. Makoto walked towards the accident site, unable to believe his eyes. What he found was a bent and broken can of juice - the cause for the motorcycle overturning, and one of that cans that Makoto accidentally spilled all over the streets just a while ago, and one that he wasn't able to locate when he searched for missing cans.

It was a series of impossible coincidences caused by Makoto's bad luck. And this situation was merely a result of Makoto's overwhelmingly bad luck managing to defeat Jutarō's careful planning and luck. It rendered all sorts of talent and hard work futile.

The letter addressed to that year's Ultimate Lucky Student burnt up in the accident. Hope's Peak Academy's headmaster, Jin Kirigiri, decided to hold the lottery again because he felt that the misfortune of having her admission letter burnt up disqualified her from being accepted as Ultimate Lucky Student. In fact, he already got the results of the draw - Makoto Naegi.

Meanwhile, Makoto was returning home after a long period of questioning by the police (and of course, he missed Sayaka's performance on the TV that he was looking forward to). He was dead tired, yet his nerves were still on the edge as he was wary of more unfortunate things happening to him on the taxi ride home. Fortunately, he arrived home rather smoothly - only to be greeted by enthusiastic Komaru, who told him that a letter from Hope's Peak Academy had arrived for him, accepting him as this year's Ultimate Lucky Student.

Makoto was overjoyed - he felt like all the misfortune that he'd experienced in the day had been overturned by this news, but little did he know that he was wrong.

Episode 05 - The Beginning of the End
Makoto is seen entering Hope's Peak Academy for the first time on a sunny March day. Unknowingly, Junko and Mukuro are behind him, plotting the first stages of their plan.

Episode 11 - Goodbye, Hope's Peak Academy
Makoto once again appears, talking to Sayaka as the rest of the students seal the school. Junko, considering his luck a threat, throws a wrench at him without anyone noticing, but Makoto slips on a piece of paper, causing the wrench to miss him. Junko (faking concern) and Sayaka ask if he's alright, which he confirms. As they walk away, Sayaka warns Makoto help would be hard to get should he get injured, but Makoto assures her that he's fine and that their ordeal will be over soon anyway.

Chapter 3
During his first year at Hope's Peak Academy, Makoto found an e-Handbook Yasuke Matsuda had dropped. When he went to the medical bay to return it, he bumped into Ryoko Otonashi, who asked him where Yasuke is. Makoto answered that the Ultimate Neurologist was probably out before trying to comfort Ryoko when she launched into a rant of frustration. Both students were confused by each other; Ryoko suspected Makoto of being a pervert behind his friendly demeanor, while Makoto found Ryoko to be a bit familiar. He introduced himself, explained what he came to do, and tentatively told Ryoko about a rumor regarding a student who has become forgetful. Hearing that, Ryoko continues to ask persistently if he used to know her, until he finally admits he did.

Suddenly, Misshiki Madarai appeared, grabbing Makoto's shoulders. He claims to be immortal and a survivor of the student council, looking for revenge for the student council as well as his own pride, willing to do anything. As the other two talk, Makoto is completely silent and terrified. Madarai then turns expressionless, as he remembers Makoto. He asks his name and seems to threaten him, and the other boy is very afraid. Madarai tells Ryoko that Makoto's head will be crushed in an "unfortunate accident" if she doesn't obey him and tell him what he wants. Madarai looks at her with intimidating eyes while Makoto pleads to her silently. Ryoko then calms down as she begins to mumble her usual mantra, that it has nothing to do with her. Both boys are confused by her words, and she simply answers that Makoto is unlucky, like he himself mentioned before. To prove his point, Madarai is about to kill Makoto, but suddenly his classmate Mukuro appears and saves him by attacking Madarai. Very relieved, Makoto thanks the girl, and she answers that she was simply helping her classmate and happened to pass by. Makoto continues his sincere thanks, much to Mukuro's embarrassment. Makoto thinks he's lucky because Mukuro happened to pass by.

After an awkward silence, Mukuro notices someone was hiding close by, and it turns out to be Yuto Kamishiro. He claims Ryoko is his client and he asks her to come with him. When Makoto says they should do something about Madarai on the floor, Mukuro says she'll do it. Makoto is worried and thinks she shouldn't do it all by herself. Yuto agrees they shouldn't tell the security department about it, as he and Ryoko are busy with their case. Yuto is angered by Makoto's hesitation and leaves with Ryoko in a hurry. As they leave, Makoto looks at Ryoko with determined eyes and Ryoko feels uneasy as she can suddenly feel an incredible aura coming from him. It is Ultimate level of hope, though she doesn't realize it and in a few minutes, she completely forgets his existence.

During the Tragedy
Makoto lived in the Academy happily, spending his happy times together for around one year until The Tragedy occurred. During The Tragedy, Jin planned to seal the school building and let the students live forever inside the Academy in order to protect them from the destruction. His plan was agreed by Makoto and the rest of the class, and they sealed the building together and lived peacefully inside it for a year without knowing that the Ultimate Despair members were already in their midst.

The True Ultimate Despair took away the Class 78th's school memories so they could participate in the Killing School Life.

Prologue - Welcome to Despair
Makoto is first seen in front of the building of Hope's Peak Academy. When he makes the move to enter the school and begin his new life, his vision suddenly becomes warped and blacks out. He wakes up in a classroom with bolted windows with little explanation beyond a crayon-written letter.

Makoto soon finds out that he is not alone in what he assumes is the academy; a group of other students were locked in with him, each telling a story with one thing in common: they all woke up somewhere in the school after losing consciousness when stepping inside the school grounds. Without any other options, Makoto joins the present students as they assemble and are introduced to Monokuma. Monokuma gave the students a harsh choice: either live in the academy forever, or kill one of the other students without being found out to “graduate.”

Chapter 1 - To Survive
After Makoto woke up from getting knocked out during a scuffle in the assembly, Monokuma announced to all the students that he had prepared a "gift" for them. The "gift" ended up being a DVD containing an incentive personalized to each viewer: Makoto's DVD is of his sister and parents at home smiling at the camera wishing him luck, then suddenly cutting to the room destroyed and his family is shown missing. Sayaka reacted the worst out of all the students and fled the room in a panic; Makoto followed her and was able to calm her down by promising to keep her safe.

Unfortunately for Makoto, his promise to protect Sayaka was broken that same night. They had switched rooms for the night because of Sayaka thinking it would be safer, but when Makoto awoke and checked on her, he instead found her corpse in his shower. The presence of the corpse in his room led Makoto to be blamed for the murder. He was in shock.

In Makoto's frantic quest to clear his name, he worked through numerous heated debates and collected evidence. Kyoko showed him a note from Sayaka revealing that Sayaka had suggested the room switch with the intention of luring Leon Kuwata there and murdering him, framing Makoto for the murder. After Makoto arrived at the most logical conclusion of events that had transpired leading up to the murder, he had an intense debate with Leon. Leon was found guilty of Sayaka's death, leading to Makoto's name being cleared from the murder. Leon was then dragged off to his punishment by Monokuma.

After witnessing Leon's brutal execution-by-baseball-machine, Makoto angrily blamed Monokuma for causing Leon and Sayaka's deaths. His emotional outburst was, however, halted by Kyoko, after which Makoto remained sullen and silent.

Kyoko suggested that Sayaka's motive in writing her dying message could possibly have been to protect him, and that she had misgivings about her plan to murder Leon. Makoto responded that he would shoulder the weight of both Sayaka's and Leon's death and live on, so their deaths would never be forgotten, and so that he could avenge their deaths by finding out who the mastermind was.

Chapter 2 - Boy's Life of Despair
Since the death of both Sayaka and Leon, Makoto, along with the others, seek for more clues in order to find a way to escape. However, Monokuma gave another incentive to the students, the students' most embarrassing and the deepest secrets. During the course of doing so, he witnesses another death which involved his friend, Chihiro Fujisaki, who was hung like a crucified figure nearby a blood message on the wall. With the assistance of Celestia Ludenberg and Mondo Owada's information about the clue, Makoto manages to clear both Byakuya's and Genocide Jack's name off the crime and finally pins Mondo as the culprit over Chihiro's murder.

Despite Kiyotaka Ishimaru's pleas which claimed that Ultimate Biker Gang Leader was innocent over the murder, Makoto solidifies the charges by noticing the changed gym rooms and the bloodied dumbbell. He, however, didn't anticipate that Mondo's reason to kill Chihiro was due to his jealousy and rage over Chihiro's strong determination to get rid of his weakness. After Mondo's execution, Makoto witnesses a sense of distrust among the group as they wondered who would be the next victim of the next murder.

Chapter 3 - A Next Generation Legend!
The next day, Makoto joins the surviving students as they gather for Monokuma's announcement. He is then shocked to learn that whoever graduates would be given ten billion yen, and grows frustrated as he realizes the intentions of the bear to turn them against each other. After the assembly, Makoto and the others gather in the bathroom after hearing Aoi exclaiming that she had seen Chihiro's “ghost” there.

Instead of seeing a ghost, however, Makoto and the rest of the students discover an AI programmed by Chihiro called Alter Ego, who was made to resemble its creator. Amazed and in awe, Makoto is filled with hope by their sudden advantage and remarks about how Chihiro has left a bright legacy for them. Later, Alter Ego turns up missing, leading Makoto and the rest to meet a roadblock again as they learned from Byakuya that whoever stole Alter Ego was most likely a traitor. Makoto and the others then decide to search for the AI.

Makoto's search for Alter Ego comes to a halt as he hears Celestia's scream, claiming that she was attacked by a suspicious figure known as “Robo Justice.” Celestia, stating that she has a clue, shows them a picture of the figure via Hifumi Yamada's digital camera. Worried that the culprit would hurt his friends again, Makoto then rushes to warn Kyoko and the others about the new threat, only to find an injured Hifumi instead. Once again, trying to find the others so that they would be informed of recent events, Makoto wanders around and discovers Kiyotaka's corpse lying on the floor.

After a period of investigating, a Class Trial begins with accusations against Yasuhiro Hagakure, who was the primary suspect. The debates go on and slowly, Makoto uncovers the truth and reveals that Celestia is the culprit of the murder. After saying the reasons why she killed their classmates, Makoto and the other students watch on as Celestia is executed.

Chapter 4 - All●Star●Apologies
After the 3rd Class Trial and Celestia's execution, Makoto asked Kyoko where she disappeared to during their search for their absent friends, Kyoko then tells Makoto that she discovered a secret room in the men's room on the second floor. Knowing that Makoto heads toward the secret room after the nighttime announcement.

Makoto discovers that behind the supply closet and finds shelves filled with many files and some old yearbooks, all covered in dust. Interestingly he found a file known as “Hope's Peak Academy Student Register,” the only things that isn't coated in dust. When Makoto opens the file, he finds a single scrap of paper written “YOU MUST NOT LEAVE THIS PLACE.” Makoto recognizes its words, but before he can remember anything, someone who wears a mask and a lab coat attacks him from behind and succeeds in making him lose consciousness.

In the aftermath, Makoto found that all the files in the shelves, and even the single scrap of paper, are gone. But Makoto decided to rest his head and body first, so he decided to head back to his room. However, when he reaches the first floor, he hears a noise in the gym and it was revealed that the noises were made by Sakura Ogami and Monokuma who were fighting all night, discussing about “Mole” and “Hostage.”

Makoto could feel the unease of the confrontation which he assumes that Sakura has hidden something; it's revealed later that Sakura is the mole among the groups. Sakura commits suicide to prevent the dispute among the groups. And her sacrifice was not in vain as the others stop fighting each other.

Chapter 5 - 100 Mile Dash; Pain of a Junk Food Junkie
After witnessing his friends falling one by one, executed and murdered, Makoto vowed to his late classmates that he would find the clue to escape this nightmare so that their deaths would not be in vain by finding the real culprit behind the inhumane game.

While in his sleep, Makoto is suddenly attacked by a masked figure but is saved by Kyoko. Before he checked the school for more mysteries, Makoto finally found the perpetrator who was almost responsible for his assassination, only to find that person dead.

During the investigations, Makoto also found the control room, only accessed by Monokuma and decides to investigate. Later he realized that Monokuma is much like a mass-produced robot and he is indeed surprised that all the commotion they had been through were. As the clues pointed to Kyoko, Makoto refused to accuse her of the murder. This decision sadly didn't help him at all as he is assumed to be the murderer of Mukuro instead. Even with his plea for innocence, the execution is already going underway by Monokuma as Makoto has been voted guilty even though he didn't commit the murder.

In the middle of his execution, Makoto is suddenly rescued by Alter Ego, who he and the others thought were destroyed as the replacement for Sakura's “execution.” Alter Ego was able to hack into the system (thanks to Makoto hooking the AI up to the school's data server earlier) and rescue Makoto by stopping the slammer and opening a hole beneath him that sent him to the basement. Having escaped death, Makoto wakes up in the basement and decides to conserve his energy.

Makoto is later awoken by Kyoko falling into the basement to rescue him. She ends up using the Master Key she found in the principal's office and they both make their way back up by climbing a tall ladder. On the way up, Kyoko tells Makoto that she remembers parts of her past and who she is. She then reveals her identity as the “Ultimate Detective,” and informs him that she came here to find her father, the principal, who abandoned her when she was a child.

Chapter 6 - Ultimate Pain, Ultimate Suffering, Ultimate Despair, Ultimate Execution, Ultimate Death
After his surprising return with Kyoko, Makoto is reunited with the other students (In the game, the other students still think that Makoto was responsible of killing Mukuro until he and Kyoko convinced them that it was a trap created by Monokuma, who was in fact the true killer; In the anime, however, the other students realized that Makoto was innocent, as well as Monokuma being the true killer and breaking his own rules, when Alter Ego saved Makoto from his execution. This caused them to feel guilty for not trusting Makoto and nearly killing him for a crime he didn't commit. However, Makoto forgives them, saying that it was Monokuma's fault for breaking the rules and trying to make them all feel despair).

Kyoko then explains on his behalf that the trial was restarted due to some circumstances (namely, her sharp retaliation over Monokuma's taunts). Throughout the course of the investigation, Makoto learns about their past via the DVD and is confused that all of the students, including himself, agreed to stay in the academy during their interview with the former principal of Hope's Peak Academy, Jin Kirigiri; they began to realize that they were actually having amnesia before the sadistic game started and they had been staying in the academy for two years.

When the real Junko is revealed to be the true perpetrator, Makoto and the other survivors are confused by the reasons behind her sadistic survival game. With some details revealed by Genocide Jack who, unlike her alter, Toko, had retained her memory, Makoto is able to look back at the events of the Killing Game and how Junko's plans had been successful:
 * Sayaka's interpersonal reasons to frame Makoto by murdering Leon out of desperation to leave the school and save her idol group (though Leon instead retaliated and caused her plan to backfire, she then wrote Leon's name in her own blood, which was thought to be the number 11037 due to it being written backwards, as a redemption for her betrayal).
 * Mondo's anxiety about his secret (his brother's death) exposure in order to keep his motorcycle gang together and accidentally kills Chihiro due to his uncontrolled rage and jealousy over Chihiro's inner strength.
 * Celestia's greed for the 10 billion yen so she can buy a European castle, including her fantasy about vampire butlers, would lead to her treachery to the group by killing both Kiyotaka and Hifumi.
 * Sakura's suicide due to her position as a mole worked for Junko and caused the conflict and distrust behind the group. (Though at first, it seemed that her suicide was caused by the beatings from Yasuhiro and Genocide Jack, it was later revealed that the act was her last ditch effort to keep the group together from turning against each other).

At the climax of the trial, Makoto and the rest were stunned by Junko's revelation about Hope Peak Academy's true plan, which was to plant ultimate despair into the world. Junko then again twisted the rules in an attempt to bring out despair from the survivors. In that attempt, she stated that if they chose to live a life in which they can survive, then Makoto would have to be executed. Yet as persistent as always, Makoto refused to give in and tried to persuade his friends that hope still exists in their hearts.
 * He convinced Yasuhiro that staying in the school, chained by their own despair, isn't really living at all. Yasuhiro then realized that living means moving forward, even if it's hard and scary; thus, he renewed his desire to leave the school and find his future.
 * He convinced Aoi that they aren't just living for themselves, but also for their deceased friends. Aoi then realized that Sakura, her deceased friend, would say that living means going against despair and walking through hardship; thus, she decided to move forward in memory of her fallen classmates.
 * He convinced Byakuya that the Togami Family never succumbs to despair and he, as the heir, must rebuild it as many times as he can without giving up. Byakuya realized that the Togami Family isn't dead since he is still alive. This made him decide to keep his word and have the mastermind, Junko, defeated and dead (although he insisted that he wasn't doing this for Makoto).
 * In the game, Jack told Makoto that she doesn't really care whether she stays or leaves, so as long as Byakuya comes with them. In the anime, Jack decided to leave as well after seeing Byakuya convinced to leaving the school and ending the mastermind's life.
 * Finally, Makoto convinced Kyoko that her father never gave up nor gave into despair; if there is no hope, then they'll become the new hope. Kyoko realized that her father would never sacrifice Makoto for the sake of his own life; she also realized that she could understand her father even if blood was the only trait they shared. With this revelation, Kyoko announced that Makoto himself had a hidden Ultimate talent: as someone with the ability to defeat Ultimate Despair, he could be called the Ultimate Hope.

With his classmates' support around him, Makoto managed to defeat Junko; much to his surprise, she gleefully accepted her defeat. He tried to dissuade Junko from killing herself, but she eagerly relished the chance to experience the absolute despair of failing her master plan at the very end, leading her to execute herself in her very own special punishment (The Ultimate Punishment). With Junko gone, the survivors were finally free from the strings of the Killing School Life.

Epilogue - Goodbye Despair Academy
With their torments finally over, Makoto then opened the door that led to the exit while beginning to wonder if his doubts and insecurities remain in his mind after his gruesome journey in the academy. In his heart, however, Makoto remarks that as long he refuses to give in, hope will spread throughout the world and as long he wields hope, he would make the impossible possible.

Joining the Future Foundation
Makoto and the others survived together in the apocalyptic world until they were found by the Future Foundation. They decided to join Future Foundation to fight against despair and Future Foundation helped them to recover their school memories. Makoto became a member of the 14th Division. Despite not being a branch head, his exploits are famous enough that he was recognized by the audiences of Serial Killer Gambling.

Chapter 2 - Legend of the Revolution
Makoto was seen in the end of chapter 2 after Komaru and Toko succeeded in contacting Future Foundation on top of Towa Tower.

Chapter 3 - Cute Girl's Battlefield
Komaru and Toko contacted Future Foundation after they defeat Jataro Kemuri, one of the Warriors of Hope's main members. Makoto is the one who responds to the device, surprising Komaru. She asked about their parents' condition, but Makoto didn't know about their current situation and where were they. Makoto explained that he joined the Future Foundation, and was surprised that Komaru was with Toko who had suddenly disappeared. It was revealed that Toko went to rescue Byakuya without any orders from Future Foundation. Komaru who realized that both Makoto and Toko already knew each other, and she wondered why Toko didn't tell her anything.

Makoto was glad that his sister was with Toko, but Toko was mainly concerned with Byakuya being put in danger. Makoto later explained to Komaru about his, Toko's and Byakuya's time trapped in the Killing Game at Hope's Peak Academy, and how all three of them had joined Future Foundation. Makoto's explanation awed Komaru who lauded the survivors for fighting and moving forward unlike herself. Makoto ended up on the receiving end of Toko's jab about him becoming Ultimate Hope and pulling everyone together. Komaru remarked on Makoto's growth, saying that Makoto had become more mature and reliable than he used to be.

Makoto apologized to Komaru about her imprisonment, explaining that she, like other captives who were related to Class 78th, were used as motives for Class 78th's students to turn against each other. He also explained that after a long period of fruitless searching for the captives, they had received an anonymous tip only days prior, told that Captives from the Killing Game were being held in an apartment tower in Towa City. He explained that that was the reason Byakuya mounted the rescue mission in Towa City, not expecting that Towa City would simultaneously collapse into chaos and for Byakuya to end up missing. Makoto was alarmed when Junko Enoshima's name was mentioned by Toko in reference to the girls running into the Warriors of Hope; the Warriors were catching, releasing, and then hunting Captives bound to wristbands they made, that self-destruct when their wearers exit Towa City, and that Byakuya's capture was a deliberate trap set by the Remnants of Despair to lure the Future Foundation into action at Towa City. Makoto believed that Junko had foreseen this desperate situation from the very beginning.

Toko forbids Makoto from rescuing Komaru as it would put Byakuya in danger and declares if he came, she would take Komaru's life. Panicked, Makoto attempts to calm Toko down and calls Komaru's name before the connection lost. Nagisa Shingetsu, the Warriors of Hope's replacement leader at the time after Masaru Daimon's "death," spotted them and scrambled their device by strengthening the jamming signals.

Epilogue - The Changing World We Made
Makoto was contacted by Byakuya, who proceeded to explain that Komaru has chosen to remain in Towa City of her own volition, then watched a handheld recording on Byakuya's device of Komaru explaining her reasons for remaining in Towa City (not specific, but likely referring to Toko). He remarked that Komaru had surprised him before and that he resolved to intervene directly in similarly drastic situations; this remark served as a retrospective explanation for Makoto trying to save the Remnants of Despair in Danganronpa 2.

Chapter 6 - This is the End; Goodbye Academy of Despair
When Future Foundation found the remnants of Ultimate Despair, Makoto protected them and decided to undo Junko's influence by putting them into the Neo World Program.

During the last trial, Monokuma summoned a fake Makoto to lead the students to choose the "graduation" so Alter Ego Junko's could succeed her plan to create her "Junkoland."

However, Hajime Hinata knew that "Makoto" was the fake one. The real Makoto returned along with Kyoko and Byakuya to save the remaining students, and after much trouble was finally able to activate the Forced Shutdown.

Epilogue - The Day Before the Future
After Alter Ego Junko is seemingly destroyed in the Forced Shutdown sequence, Makoto, Byakuya, and Kyoko leave the island, hopeful that the Remnants of Despair had been rehabilitated, despite not being guided in the expected direction of "Hope" but a "Future."

Danganronpa 3: The End of Hope's Peak High School - Future Arc
After returning from Jabberwock Island, Makoto was charged with the crime of treason for protecting the Remnants of Despair. Everyone who gathered for Makoto's trial was trapped and thrust into the “Final Killing Game” by Monokuma. Everyone is fitted with a strange bracelet that releases a sleeping potion at a fixed time. While asleep, the traitor in their midst kills a Future Foundation member. To survive, they'll have to ferret out the traitor and stop the killing.

Makoto's NG code is "Running in the hallway." However, it can be sidestepped by having other people run while carrying him, or by running inside a room.

Episode 01 - Third Time's the Charm
Makoto arrived at the rooftop of Future Foundation's off-shore facility, where Kyoko, Aoi, and Yasuhiro were already waiting for him. He has been arrested by Future Foundation due to his action that against their protocol and deceived them.

Arrived at the boardroom, Kyosuke Munakata requested Juzo to handcuff him. Juzo sarcastically apologized to Makoto for having to do this to the great "hero" who brought down Junko Enoshima. When Makoto tried to respond, Juzo punched him in the stomach, declaring that none of them deserved to be called heroes after the amount of their comrades they sacrificed. He continued to assault Makoto until Great Gozu asked him to stop, before threatening him with violence if he continues. When people in the boardroom began to argue, Kyosuke ordered them to calm down and temporarily suspended the board meeting so that Makoto can be treated for his injuries sustained from Juzo.

Chisa Yukizome visited with Makoto in a separate room to help disinfect his injuries. Makoto asked if she was a doctor, and Chisa revealed that she was the homeroom teacher of the Remnants of Despair. She asked why he wanted to protect them despite what they had done, and nods after hearing his answer. She said that they were right to call him the Ultimate Hope and said that, like Makoto, Kyosuke is also Future Foundation's hope. For that reason, she didn't disagree with Makoto's feelings but understood that Ultimate Despair can't be combated by just being nice, which is why Kyosuke's decisiveness is so important. She told Makoto that if he could try to understand Kyosuke it would make her happy, and she hoped that the two of them could combine their hopes for a greater hope.

Makoto and Chisa returned to the boardroom when the building attacked by an unknown enemy. Kyosuke who still suspect Makoto ordered Juzo to restrain him. As he and Kyoko confirmed that they were locked up inside the facility, all of them rendered to sleep after a sleeping gas cast inside the room.

Sometime later, Makoto woke up to find that he was wearing a wristband with a countdown timer, unsure of what it could mean. His thoughts were cut off by Monokuma's laughter, who then appeared on a monitor addressing the whole group. He stated that, as a reward for all of their hard work trying to combat despair, he was going to have them all kill each other. Makoto shouted at Monokuma, saying that he would never play his game again and that they wouldn't kill each other because they were comrades.

Kyosuke realized in a panic that Chisa wasn't in the room with them, and asked the group where she went. He and Makoto noticed the blood dripping from the ceiling and the two look on in horror to find Chisa's dead body draped over the room's chandelier. Monokuma cheerfully told Makoto that he had no say because the game has already started, and the weight of Chisa's corpse caused the chains rooting the chandelier to the ceiling to snap. Makoto watched Chisa's body in horror, eventually replay the same experience he had during the Killing Game of Class 78th.

Episode 02 - Hang the Witch
To make everyone stick together, Makoto told everyone to work together after Monokuma announced the rules of the Final Killing Game. He also wanted to find the attacker but unlike the others, he didn't want to kill them and instead suggested to restrained them somewhere. Juzo angered at Makoto's words, about to using violence against him. Aoi stood up for Makoto along with Ryota Mitarai. Juzo's violence resulting Daisaku Bandai's death who accidentally violated his NG Code (witnessing violence by participants).

Seeing this accident, Kyosuke decided to make everyone vote for the attacker and almost all of them pointed at Makoto. Despite not knowing if Makoto was truly the attacker, Kyosuke and asked him to cooperate as Juzo took out his knife to stab Makoto. Great Gozu stepped in and protect Makoto from Juzo's attack. Kyoko soon created a diversion using the fire extinguisher, allowing Makoto to escape from the boardroom along with Aoi.

In the hallway, Makoto can't catch up with her since his NG Code wasn't allowed him to run in the hallway. Seeing no other way, Aoi offered him to ride her on her back and tried to find a place to hide. Kyosuke managed to hold back Gozu's attack and catch up with Makoto and Aoi. Miaya Gekkogahara later came to their side and showed them a safe place to hide. Gozu quickly leaps and dropping the floor, slings over Makoto on his shoulder. At the last seconds, Makoto managed to close the door before Kyosuke's flying sword slashed him.

Makoto, Aoi, Miaya, and Great Gozu decided to barricade themselves in a room few minutes before the time limit hit. Makoto sits beside Aoi and tried to comfort her not to worry again since they will always be fighting despair together. Just before the sleep drug injected, Makoto wanted Aoi to believe in his luck.

Makoto woke up sometime later and found a trace of blood on his hands. When he looked at Aoi, he was very surprised and terrified seeing a knife stabbed on her chest.

Episode 03 - Cruel Violence and Hollow Words
Makoto was very shocked upon discovering Aoi's body. However, it turned out that her death was faked by the attacker as he saw Aoi awoke from her sleep. He found out that the knife was merely a toy and the splattered blood was came from tomato sauce. Later, they found out that the one who was killed by the attacker was Great Gozu.

Makoto was very sad and remembered Gozu's words to always have faith on his hope. Later, he and Aoi took down his body and Aoi put her jacket on Gozu's dead body in respect. Makoto planned to talk with everyone to cease the disputes between the Future Foundation members. Miaya then suggested him to use the intercom system of the facility.

On their way to the intercom room, Makoto noticed that Miaya turned in a circle when she met with an intersection and asked her if her NG Code didn't allow her to turn right. Miaya was surprised after Makoto revealed her NG Code, afraid that Makoto and Aoi already planned to kill her.

Makoto calmed her down, stating he would never hurt her and showing her his NG Code as well, immediately followed by Aoi, making Miaya referred them as her soul mates. When they heard someone was coming, Aoi and Miaya created a diversion so that Makoto can safely reach the intercom room. He left the scene and hoped for their safety.

Reaching the intercom room, Makoto announced via the speaker Great Gozu's death and the motive behind his action to protect the Remnants of Despair. He explained how he found them and took them into custody, knowing full well that they were the Remnants of Despair. He did this because he believed they must have once been normal students of Hope's Peak Academy, filled with hope until Junko Enoshima corrupted them into despair. He also explained how he'd hoped to rehabilitate the Remnants with the Neo World Program until Alter Ego Junko infected and messed with the program. He told that he abandoned the game and wanted to talk with everyone in the intercom room. He finally revealed his NG Code being not to run in the hallway and ended his speech.

The first one to came to the room was Kyosuke who broke the window using his sword. Makoto stands firm and said that he only wanted to talk with him. In the room, Kyosuke revealed his true intention to kill Makoto was to prevent the attacker who might be ended the Final Killing Game before they revealed their true identity and used Makoto's hope to corrupt people with greater despair. Kyosuke revealed his point of view of "hope," stating that no one can talk about hope before he experienced the true despair. Makoto angered by Kyosuke's words who said that the Killing Game he experienced before was merely a game for him. Unlike Makoto, he was outside the Killing Game, facing the Tragedy with his friends while Makoto trapped inside Hope's Peak Academy. In the last scene, Kyosuke was able to capture and tied Makoto.

Episode 04 - Who is a Liar
Makoto was tied inside the intercom room when Kyosuke announced to everyone that he will execute Makoto immediately. Kazuo Tengan, Aoi, and Miaya came to the scene to rescue Makoto. Kazuo believed that keeping Makoto alive is an important matter and truly believed that he is the Ultimate Hope whose hope could defeat despair. Makoto grabbed on to Miaya's wheelchair and started to escape.

Until they reached a point, Makoto and Aoi prevented Miaya from volunteering herself to stop Juzo in the hallway. Miaya insisted on going, saying that maybe she was already affected by Makoto's "hope."

Episode 05 - Dreams of Distant Days
Makoto and Aoi encountered with Juzo after he successfully knocked out Miaya. Makoto told Aoi to run but she refused and instead took a metal pipe and stood against the former Ultimate Boxer. As Miaya reactivated again by her controller, Monaca, she could distract Juzo's attention and once again Makoto jumped to Aoi's back and escaped from the scene.

Episode 06 - No Man is an Island
Makoto having a nightmare during his sleeping time. He dreamt that Kyoko was dead beside him with Kyosuke saying that her death was his fault, thinking that he could go on without sacrificing someone precious to him. He awoke and found himself still alive with Aoi and Miaya on his side. However, he worried about the third victim. Miaya then searched for the third victim via the security-camera system.

Makoto was shocked when Miaya discovered Kazuo's body. She cleared the fact that Kazuo was not killed by the attacker, but by Kyosuke Munakata judging from the slash wound on his neck. Makoto saw his dying message, "I trust the hope of the world to you," which Aoi stated that Kazuo referred to Makoto.

Makoto broke down and left speechless. The controller of Miaya, Monaca decided to encourage him and eventually pushed Makoto to bring a brilliant idea, that is to break the building's wall. Miaya suggested them to contact the Future Foundation on the outside and their signals reached Byakuya's place.

Makoto informed that he, Aoi and the others were trapped inside the off-shore headquarters and forced to participate in the Final Killing Game. To his surprise, Byakuya didn't know about the fact, proved that Monokuma was lying about the broadcast tot he worldwide of the Killing Game. In turn, Byakuya informed to Makoto that Kyosuke already sent his troops to annihilated the Remnants of Despair in Jabberwock Island regardless the outcome of the meeting. As the call ended, Makoto encouraged by Byakuya to stick together with his former classmates.

At the end of the episode, Makoto regained his confidence back and keep holding his faith to his friends and family.

Episode 07 - Ultra Despair Girls
Waiting for Byakuya's call, Makoto and Aoi surprised when Komaru appeared on Miaya's computer screen instead of Byakuya. He was glad to see her sister was okay but then became worried as Komaru informed him that according to Monaca, one of the survivors of the Killing School Life might die because of him.

Episode 08 - Who Killed Cock Robin
Makoto and Komaru continue to discuss Monaca's information about someone who survived 'Big-Sis Junko's Killing Game' and they will die because of Makoto.' Makoto talks about how Komaru has grown mature and she requests he comes and gets her when the mess he's in is over. After the transmission ends, Miaya Bot begins to re-boot and Makoto realizes that this Miaya, is in fact, a robot. Aoi rushes him out of the room through a gap in the wall, reminding him that his NG code only states he can't run in the hallway's but they encounter Kyosuke around the corner and Makoto is frozen in shock. Miaya Bot, after her re-boot, steps in to aid Makoto and Aoi and gives them an opportunity to escape. Aoi boosts Makoto onto her shoulders and carries him away from the scene to find Kyoko.

Episode 09 - You are My Reason To Die
Makoto and Aoi soon find Kyoko who is discussing with Ryota how Makoto was her savior when she was in trouble, although she stops mid-sentence as soon as she notices a blushing Makoto and Aoi.

They all enter an unknown room to eat and drink before the time limit goes off, Makoto seems to be worried that his words don't seem to have much effect and that Byakuya might be in danger after Monaca's information on someone dying because of him. Kyoko gives him comforting support which invigorates him to keep doing his best.

Both Makoto and Ryota try to push a large object in front of the doorway before the sleeping drug comes into effect but they both fail to make it budge until Aoi moves it for them. Kyoko encourages Makoto one last time before the sleeping drug causes them to go unconscious.

Upon awakening, Makoto is pleased to find everyone had seemingly survived, though when he notices Kyoko motionless on the floor and finds her NG code has been set off he bursts into tears over the realization that it was his fault that she got poisoned. Kyosuke cuts in over the intercom and explains to Makoto that Kyoko's NG code proves his platitudes are useless and requests another battle, over who's hope is worthy. At first, Makoto seems in shock but ends with a determined face through all his tears.

Episode 10 - Death, Destruction, Despair
Makoto recalled the time of when he became stuck in the trash disposal room after his execution failed, during the Killing School Life. He remembered when Kyoko came down to save him. After remembering this moment, looking at Kyoko again, he wiped the blood of her left eye onto his left-hand palm, determined to settle everything with Kyosuke. He walked to the door and told Ryota to wait for Aoi. Ryota wondered how Makoto could easily accept the fact that one of his dear friends died and isn't overly saddened by it. Makoto grimaces before turning around and replying with his smile, saying that he, of course still can't get over Kyoko's death but that she entrusted her hope to him and he has to fulfill her faith in him. Makoto tells Ryota that Kyoko kept him alive by not telling him her NG Code because she knew that he would do something reckless if she told him. So Makoto decides he has to keep moving forward, and his decision is supported by Aoi who states she 'believes in him.'

Makoto leaves the room and makes his way to the hallway, he begins to cry once more before wiping away his tears, stating that being optimistic is the only good trait he has. As Makoto continues down the hallway, he notices Miaya bot has been sliced in half and is automatically shocked at the immense power of Kyosuke. Makoto seeks to stop Kyosuke, while Kyosuke seeks to save Makoto. Soon afterward, Makoto arrived in the monitoring room and stated that he wouldn't hesitate anymore, and requests working together with Kyosuke to end the 'game.' This prompts Kyosuke to attack with all his might, finding Makoto's words useless. The Ultimate Hope dodged the opening strike and ran from the monitoring room, shutting the door behind him - Kyosuke simply broke one of the windows and gave chase. Makoto then lured him to a trap and he followed his quarry into a room, where he found that Makoto had flooded the ground with water, trying to electrocute him to death with a stray wiring. Kyosuke was fast enough to neutralize the tactic by using the heat from his katana, also injuring Makoto's leg with Kazuo's chuusen. However, the resulting steam cloud from the evaporating water bought Makoto enough time to escape once again.

Makoto hurries down the open hallway to the safety of another room, filled with debris. During his escape, Makoto found a fire hydrant and went into hiding to make a surprise attack. However, his surprise attack was easily thwarted by Kyosuke who followed the blood trail of his leg injury. He tossed the fire extinguisher aside and commented that Makoto had run out of luck - moments later, the fire extinguisher suddenly bursts from the build-up of foam behind it and hits Kyosuke in the back, giving Makoto a chance to attack, lunging at Kyosuke from the mist. After a short struggle, Kyosuke finally seemed to have Makoto at his mercy - however, he stopped the fatal swing of his sword at the last second. He had finally realized his quarry's true intention: trapping him in a room with a closed door being the only exit. As Makoto explained a moment later, Kyosuke's forbidden action was "opening doors;" if he killed Makoto, he would be trapped in the room.

The tired Makoto is slammed into the wall by Kyosuke who demands to know when he was first tainted with despair. Makoto then heard Kyosuke's revelation about what Kazuo had told him after their fight: any member of the Future Foundation could be the traitor, even Chisa, which is later proven true as Chisa confessed herself to being a member of Ultimate Despair via photos that she left. He reiterated his intent to destroy despair, even if he had to sacrifice his loved ones, only for Makoto to counter that hope could not come from solely eliminating despair.

Makoto's claim that he should not forget Chisa enraged Kyosuke, making him launch a flurry of punches, furiously insisting that Makoto knew nothing of the pain of having someone that they loved tainted with despair. In response, Makoto admitted that if the roles were reversed and he had to kill Kyoko to stop despair because she had killed others, he would not forget the good times they had had before they were set against each other. The Ultimate Hope's words stirred Kyosuke's memories of Chisa at Hope's Peak Academy, finally making him understand that his view was incorrect. Finally dropping a bloodied Makoto to the floor, Kyosuke gave a scream of grief before collapsing on a piece of rubble, crying openly and wondering how and when his beloved Chisa fell into despair.

Moments later, Aoi and Ryota came to the scene and checked on Makoto. He gently told Aoi that she should have waited for him. However, Makoto and Kyosuke are very surprised after the former announces that the killing is over; as she found a journal under Kyoko's corpse that revealed the true identity of the attacker.

Episode 11 - All Good Things
After his confrontation with Kyosuke and being told the game is over, Makoto and the rest find out that there was no attacker all along. They find out that the victims that were killed, actually killed themselves, seeing as how evidence traced towards a knife and similar wounds, they came to the conclusion that they were brainwashed into harming themselves via the monitors.

Makoto then decides to prove his theory by wrapping himself up in front of a monitor, he then reassures a worried Aoi that everything would be fine and that he promised to go save Komaru once the ordeal was over. The others then proceed to leave and as the rounds end, he along with everyone else falls asleep.

Makoto then wakes up and the monitor plays what seems to a pre-recorded video by Monokuma. All he can do is stare as the video plays on to the point where it begins counting down, he finds himself in a strange place where Kyoko and Sayaka appear. The two girls begin to taunt him, as Sayaka reminds Makoto he failed to keep his promise, and Kyoko places the responsibility for her death on him. The rest of their deceased classmates appear behind Kyoko and Sayaka, joining the two girls by taunting him.

What seems like blood spilling is shown, Makoto tries to apologize and says he just wanted all of them to be together, the scene then shows all of his deceased classmates bodies what they looked like after they had died, the scene then transitions to Makoto struggling and screaming from due to what he had just seen, a knife drops and goes out to reach it, while in his hand, the both girls tell him to join them, later the scene goes back to Makoto, who has been hypnotized with his eyes swirly and grinning. He says he'll join them, as the knife approaches his chest, it's kicked by none other than Juzo, stopping him from stabbing himself.

Juzo then proceeds to grab him by the neck, trying to get him to snap out of his hypnosis, once he returns to his usual self, Juzo then tells him that he hated Makoto and was glad when Kyosuke wanted to get rid of him, after that, Makoto notices Juzo's arm had been cut off where his bracelet was before.

Makoto then returns to the others, showing them that in fact, it was true that the whole thing had been set up in order to make everyone get rid of themselves. Kyosuke then explains that the possibility for the monitor-incident and find out that this may be had been set up Kazuo, who was most likely a despair too.

Episode 12 - It is Always Darkest
Ryota received a timed video message from Kazuo, both Makoto and Aoi gather around Ryota and watched on from his mobile phone. Kazuo explained that he was the one to set up the Final Killing Game, they are all shocked. Upon Ryota falling to the ground in anguish, he questioned whether Kazuo really had become a Remnant of Despair. Makoto tried to fill Ryota with optimism, expressing that the best thing, for now, was finding an exit although Ryota explained that he would not run away from his troubles like he had done when Junko used him for his techniques to create the Despair Video, the very one that brainwashed the Class 77-B.

Ryota concluded that he would distribute his hope video to the world although Makoto and Aoi tried to convince him otherwise. That forcing people to change was still unethical and was shredding the people of their humanity and by working together instead, hope could be spread. Ryota rebuffed Makoto's remark and explained that many people in the world have a weak resolve, unlike Makoto's resolve, which is purely unique to very few.

Ryota began to walk away, although Aoi tried to stop him, she became brainwashed after he showed her his Hope Video and brought her under his control. Ryota then commanded her to restrain Makoto, she proceeded to hold him back, stopping Makoto from reaching Ryota and putting a stop to his actions.

Ryota later brainwashed the Future Foundation's rescue squad, and they immediately sought to apprehend the remainder left within the building, so that they wouldn't be able to interfere with Ryota's plan. They are able to discover Aoi and Makoto and with Makoto still restrained, they take aim, ready to fire. Makoto commanded Aoi to run but she is still under the influence of Ryota's brainwashing video. Fortunately, Kyosuke returned in time and knocks both soldiers to the ground, saving Makoto and Aoi, they then considered a plan of action.

Makoto is able to convince Kyosuke that Kazuo may not have been a Remnant of Despair and was simply forcing Ryota's hand by setting up and putting into action the Final Killing Game. That Kazuo's hope was his belief in Ryota's talents and that he didn't expect Ryota to ever participate in the game. Upon this deduction, they are able to discover Ryota's plan of action, that he will be heading for a broadcast studio situated in a nearby building.

Soldiers approach fast and Makoto, Kyosuke, and Aoi began to run the hallways, looking for an escape. Kyosuke later acts as a distraction, giving Makoto and Aoi a chance to escape and stop Ryota. Although as they continue to run the hallways, Aoi is shot in the leg and Makoto and she sought refuge in a nearby room. After bandaging Aoi's leg, she requested Makoto leave her so he can stop Ryota and he reluctantly left although stated he would be back for her soon.

He is later cornered by soldiers of the Future Foundation's rescue squad, although with luck, Yasuhiro and Byakuya rescue him in time, to Makoto's relief.

Hope Arc- The Academy of Hope and Students of Despair
Makoto continued to the broadcasting studio where Ryota was situated, Byakuya sending half of his operatives as an escort to help Makoto break through the rescue squad blockade. They began to fire bullets rapidly, causing Makoto and Byakuya's operatives to take cover below a concrete wall. After their plan of action seemed to be halted, Nagito caused a rock slide of boulders from above, quashing the efforts of the rescue squad. Makoto is shocked to discover Nagito is the one to carry out this action.

Makoto made his way to the entrance of the broadcasting studio, finding that the Class 77-B have already arrived, he waited outside, listening intently. The Class 77-B are able to convince Ryota to discontinue his intent and allowed him come to the realization that his actions were not creating hope. Makoto, no longer needing to get involved in the situation, proceeded down the sloping platform. Stopping further down, he watched on at the breaking sunlight approaching through the skyline.

The Class 77-B left the broadcasting studio and continued down the sloping platform, Hajime nodding gratefully at Makoto with respect, responding Makoto to also nod in return. Mikan approached Makoto, wanting to speak with him although his blocked and pushed over by Nagito who began to explain how amazing it was to meet an underclassman with perhaps even better luck than he possessed, after continuing for too long he is automatically carried away by Nekomaru and Akane, Makoto smiling at the uncomfortable interaction.

Makoto later met up with Yasuhiro, Aoi, and Byakuya underneath a tent, they all greet him warmly. Makoto is relieved that all of them are okay. Noticing a video on Byakuya's laptop, Makoto and the rest surrounded the screen, Byakuya explained that the Class 77-B broadcast a message of despair, proclaiming they set up the Final Killing Game in order for the Future Foundation to still look favorable. Byakuya then congratulates Makoto, for giving the Class 77-B hope, he inherently helped towards stopping Ryota.

The Class 77-B return to Jabberwock Island, Makoto seeing them off as they leave by boat. Kyousuke then explained that Makoto needed to carry the burden of his heroic actions and his hope, which he accepts. Asking if Makoto has any plan in mind, he explained he does. Makoto then proclaimed that every day is a step forward in a world filled with hope and despair, he began to reminisce about Kyoko, staring at her blood upon his hand. Surprisingly she left the building alive, having been recovered by Mikan from a near-death state, Makoto turned around in surprise.

Several months after the Final Killing Game, Makoto and the Future Foundation decided to rebuild Hope's Peak Academy, with him becoming the principal and working alongside Kyoko.

Danganronpa V3: Killing Harmony (Demo Version)
Makoto appears alongside Yasuhiro and Hajime in the game's demo, with Makoto and Hajime working as Kaede Akamatsu's upper classmates, senior "protagonists" and major helpers.

However, the ending majorly implies that they actually worked together with Monokuma and appear to be just actors. They all compliment each other for doing good work, leave the set and mention working together in the future.

Main Story
Makoto was first mentioned as the Headmaster of the Hope's Peak Academy in a false memory shown by the Flashback Light. He was shown as the pioneer of The Gofer Project after learning that Earth and humanity are in the brink of destruction.

However, it was later revealed that Makoto and the Hope's Peak Academy's existence were a mere fiction created by Team Danganronpa in the universe of Ultimate Academy for Gifted Juveniles Series. Makoto was cosplayed several times in the last trial by Tsumugi Shirogane, the mastermind of the Killing School Semester. But somehow, Makoto and the Hope's Peak Academy's existence being mere fiction were possibly lies that Tsumugi made up, as pointed out by Shuichi at the epilogue, hinting that Makoto, his classmates, and Hope's Peak Academy's existence were real, because they're fictional but their lives are as real as Shuichi, Maki, and Himiko's lives are. Hinting that the Tragedy did happen, but not the Gofer Project.

Bonus Mode
He is playable in the game's bonus mode Ultimate Talent Development Plan.

Relationships

 * Family:

Komaru Naegi
Komaru is Makoto's little sister. Being one of the closest people to him, Makoto loves her dearly, which is proved when she is chosen as Makoto's Captive. They are also slightly similar as siblings, as they both have the same ahoge. According to Komaru, the two watch TV together, as well as share thoughts on manga they share with each other. She's also mentioned that they did argue quite a bit, which is a rather common occurrence between siblings.

When the Tragedy began, Makoto was separated from his sister and forced to participate in the Killing School Life. In an attempt to persuade the participants to kill someone, Monokuma gives them videos showing the people they cared about most get hurt or killed. In Makoto's video, Komaru and their parents were in their home congratulating him on getting into Hope's Peak Academy but suddenly disappear from their place on the couch, which has been destroyed as well as their home. Makoto was terrified, now believing that Komaru and their parents were dead, and was desperate to get out. However, when he learns Komaru is alive, he was greatly relieved and ecstatic to see his sister again. But he was a bit disappointed when she informs him that she would be staying in Towa City.

Makoto is once again contacted by Komaru during the Final Killing Game. Makoto almost despairs when he learns from Komaru that one of his friends would die because of him, but Komaru reminds Makoto that he has to stay alive so he could pick her up. This gives Makoto hope, knowing that his sister and friends were supporting him, and proudly takes notice of Komaru's growth. Although Makoto does not get a chance to tell her, he swears that he will pick Komaru up after his battle ends.

After the battle ends, Makoto supposedly reunites with his sister (although this is not shown on screen), who assists him and his fellow survivors in rebuilding Hope's Peak Academy.

His Parents
Before enrolling in Hope's Peak Academy, Makoto lived a normal life with his parents and Komaru. They are the people closest to him. This is proven when the mastermind selects them as his Captives, as well as when they are used in Killing Among Loved Ones in an attempt to motivate Makoto to kill. His parents' status is currently unknown.


 * Class 78th:

Kyoko Kirigiri
Their relationship during their school years is a bit unclear. After they were brainwashed, the two's bond began during the events of the first case. Kyoko is the one who tells Makoto that there was more to Sayaka's murder than what everyone had been led to believe. It is thanks to her words that he was able to solve the mystery of his late friend's death. She later comforts him about the events, saying that Sayaka was hesitating to carry out her planned deed to kill him and gave her (and subsequently him) the piece of evidence needed to solve the case. Since then, the two have been on good terms and she aids him in the debates during cases. Makoto refers to her as a friend and wishes that she would trust him as much as he trusts her to which she begins to try and believe in others.

During the moments of the fifth trial, when Kyoko is suspected of the crime, Makoto finds a contradiction in her claim. However, he remains quiet, putting his faith in Kyoko. This later leads to him being found guilty of the crime in question. Makoto is forced to undergo a punishment, but is saved thanks to Alter Ego. She realizes that she was only concerned for herself rather than the safety of the only person that trusted her. Because of this, she risks her life to save him. She then showed him her scarred hands, which is a great sign of trust from her, as she states that she only shows her hands to people she considers as important as family. This is coupled with other subtle hints that indicate that she has romantic feelings for him.

After joining Future Foundation, Kyoko becomes Makoto's leader. Makoto constantly makes sure Kyoko doesn't overdo her tasks and Kyoko, in return, states she'll use her powers to protect Makoto. Kyoko continues to admire his optimism, and Makoto, in turn, admires her 'cool' personality and considers her the person who has kept him alive.

In Danganronpa 3, it becomes much more evident that the two have feelings for each other, especially notable in Makoto's shyer behavior and tendency to blush more often. During the collaboration game of Danganronpa 3 and Guns Girl Z, when Kyoko is accused of being so stoic that even Makoto can't find her cute, he then a bit shyly but firmly points out that he does in fact find her quite cute, which surprises her and makes her blush. During the killing game, when Makoto overhears Kyoko talking about him with Ryota Mitarai, Makoto blushes, embarrassed by Kyoko's small speech while Kyoko coughs awkwardly after realizing he heard her. At one point, Kyoko takes off her gloves and holds his hand to comfort him, and Makoto is also seen mimicking Kyoko's thinking posture at one point. In the Otomedia magazine, Makoto is asked who is the first person that comes to his mind when he thinks about autumn. He answers Kyoko, since she is cool, but also has a really warm and gentle side. He then nervously tries to explain that he doesn't mean that in a weird way and tries to change the topic by stating that coincidentally her birthday is in October. This makes it seem even more suspicious, and he defends himself by stating that of course he would remember his own friend's birthday... only to fail to name Yasuhiro's one when questioned and nervously laughing that he may have forgotten. Aoi also appears to be very much aware that the two like each other, grinning widely after Kyoko's speech and later looking at the two while smiling knowingly, seemingly supportive of them.

However, Makoto ends up unintentionally triggering Kyoko's NG code in the Final Killing Game, as her NG code was passing the fourth time limit with him alive. Makoto was shocked and very much saddened by her supposed death, blaming himself for letting her die. However, her last words of encouragement to him seemed to give Makoto just a little bit of hope and her supposed death fueled him determination to bring an end to the Final Killing Game. Although he tried to act strong about Kyoko's demise, Makoto is seen crying about her when alone, while remembering his memories with her by his side. After he was brainwashed, he hallucinated the "ghosts" of Kyoko and Sayaka. When Makoto had a confrontation with Kyosuke it is insinuated by him that Makoto was in love with her. While trying to persuade him to help him, Makoto tearfully tells him that if Kyoko had fallen into despair, and he had no choice but to kill her, he would still be happy to have met her.

After Mikan revived Kyoko, Makoto was very happy to see her. Makoto and Kyoko are last seen running the rebuilt Hope's Peak Academy together.

In Danganronpa IF, Junko calls Kyoko "Mukuro's love rival" due to Mukuro's crush on Makoto, attempting to turn Mukuro against Kyoko. The story doesn't make clear if Kyoko was genuinely interested in Makoto or that was just one of many Junko's lies.

In Danganronpa V3 's bonus mode Ultimate Talent Development Plan, Makoto talks to her trying to help solve her issues with her father. While the two are close, the conversation is presented as friendship rather than romance.

Sayaka Maizono
Prior to entering Hope's Peak Academy, Makoto and Sayaka attended middle school together and didn't have much of a friendship due to them being in different social standards. Sayaka later reveals that she always meant to talk to Makoto since witnessing him nursing an injured crane back to health after it got lost and stuck in the pool at their school. They ended up graduating without ever having contact.

It's heavily implied that Makoto had a crush on Sayaka since middle school. This appears to be a bit naive first crush, as he doesn't actually know her at that point, but admires her from afar. He thinks Sayaka is very beautiful and, based on Makoto Naegi Secret File, he enjoyed watching her performances after she became an idol. After meeting with each other in high school, they seem to have become close friends, and are seen talking together in Danganronpa 3 - Despair Arc. Also, in one of their high school pictures, Makoto seems to be looking at Sayaka while their class was out swimming.

During the Killing School Life, Sayaka recognized Makoto immediately and befriended him. A mutual attraction formed between the two and she even considered herself to be his "assistant." He admired her very much and silently remarked on her beauty every time she smiled. They trusted one another, and she admitted to him that she would go to dangerous lengths so she can protect and defend her idol members. After receiving the alarming video which showed her friends disbanding the idol group and laying on the stage in distress, Sayaka had an emotional breakdown. Makoto was quick to comfort her, promising to get her out of the school no matter what it took. Makoto cared for her enough to let her borrow his room when she was scared of sleeping in her own. The next morning, Makoto goes looking for her, worried about the condition she was in. Upon finding her dead in his bathroom, he was devastated, letting out a loud scream and fainting in shock.

After finding out the facts from the class trial, and knowing that Sayaka took advantage of his caring actions and tried to frame him, Makoto feels betrayed; however, he still mourns over her death as she was his close friend. Kyoko comforts Makoto and tells him that it's most likely Sayaka wrote her dying message with Makoto in her thoughts, exposing her killer to apologize for her actions. Makoto points out that she also could have just wanted to get back on her killer. It is not revealed whether that is true or not, but in his conversation with Kyoko after the trial, he quotes Sayaka, calling his intuition a result of him being a psychic and then denying it as a joke after.

In the second game, Makoto used the 11037 number as a code to save the remaining students, the number which Sayaka used to save Makoto from being framed as the culprit in the first trial, Makoto later explained to Hajime the reason he set 11037 as the code because a certain person (Sayaka) left that number behind to save him from trouble, proving that Makoto believed Kyoko's theory and remembered her dearly as a friend. This is most likely due to the fact that Makoto regained his memories, and remembered his relationship with Sayaka.

In the anime version of the first game, Makoto is often seen blushing in Sayaka's company and the relationship chart confirms his crush on her. However, the chart does not mention her liking him back, while it's been implied that she does.

In Danganronpa 3 - Future Arc, Sayaka's "ghost" appeared to Makoto alongside Kyoko's "ghost," after he was brainwashed and about to commit suicide. According to Sayaka's voice actress, her appearance was supposed to represent "a guy thinking of his first love right before his death," and thus she was not portrayed with a scary voice.

In Danganronpa IF, when Makoto starts recovering his memories, he thinks that above all, he must protect Sayaka. When he gets sick, Sayaka drops her canon plan to frame him and spends the whole night nursing him instead. She's also show to feel guilty about considering her betrayal. It's also noted that when Makoto was stabbed protecting Mukuro, Sayaka was the first one to scream.

In Danganronpa V3 bonus mode Ultimate Talent Development Plan, Sayaka cooks a dish for Makoto, which he enjoys. They then talk about the old days and want to spend more time together.

Aoi Asahina
Although not sharing any kind of close relationship with Aoi when they first met, Makoto becomes close friends with her during their time together at Hope's Peak. During one of her Free Time events, Aoi requests that Makoto act as her fake boyfriend so she can practice when she gets a real one. Their closeness is also shown when Aoi is shown feeling guilty over having executed Makoto and she seems happy when he forgives her.

As members of the Future Foundation, the two have grown considerably closer. Makoto makes sure Aoi doesn't overdo things while Aoi frequently tells him that everything is okay. When Makoto is arrested for betraying the Future Foundation, Aoi (along with Kyoko) helps defend him, and she also helps him escape from Kyosuke when the latter tries to kill him. Makoto gives Aoi hope after she despairs at the fact that they must start a new round of killing.

Makoto remains with Aoi throughout most of the Final Killing Game, and she helps him escape from Kyosuke and Juzo numerous times. Makoto constantly relies on Aoi, and is thankful for the help she has given him. Despite this, Makoto worries for her safety, particularly when she attempts to fight Juzo despite being at a disadvantage due to her NG code.

Makoto and Aoi have been shown to understand one another when deaths or murders occur, even since the Killing School Life. Makoto's understanding of Aoi's emotional side is ultimately what allowed him to thwart her plans to have them executed in Chapter 4. During the Final Killing Game, when Kyoko supposedly dies, Aoi fears that Makoto would become reckless and hurt himself, despite Makoto assuring her that he wouldn't let their friend's sacrifice go to waste.

The two also comfort each other when these events occur. When Kazuo is murdered by Kyosuke, Aoi gives Makoto support and gives him hope just as he did her. After his conversation with Komaru, Makoto realizes that they may have reminded Aoi of her deceased brother, Yuta, who was Aoi's Captive and thus the person closest to her prior to The Tragedy. He appeared to want to comfort his friend, however he was unable to do so as they were interrupted by Miaya revealing her robotic nature.

During the Final Killing Game, some of Aoi's expressions indicate that she knows Makoto and Kyoko like each other, and she appears silently very happy for them.

After the events of The Tragedy have been resolved, Makoto, Aoi, and their fellow survivors decide to rebuild Hope's Peak Academy together.

Byakuya Togami
Makoto thought of Byakuya's talent as exceptional, due to his status as the Ultimate Affluent Prodigy. Byakuya often acted coldly towards Makoto, starting at their introductions, similarly to everyone else, which Makoto disliked, albeit not openly. Despite this, Makoto acted friendly to Byakuya, similarly to everyone else, keeping his negative comments to himself.

During Byakuya's Free Time events, when Makoto explained his talent to Byakuya, he thought of Makoto as a boring commoner, something which Makoto saw as going too far. Makoto tried to understand Byakuya, and he realized that that they were worlds apart. He tried, unsuccessfully, to teach Byakuya that living a normal life was alright with him. Similarly, Byakuya used Makoto to try to find out the mentality of the 99%. He offered him a $550,000 salary, as a part of a test to understand and see if his belief of being happy with what he had was true or not, and was surprised when he rejected it, but said the thought of Makoto being his secretary made him feel ill. In the end, Byakuya disliked Makoto's philosophy, but was willing to talk to him about his past, but stated they would never be friends. Makoto realized they were worlds apart, but began to understand him.

During Chapter 2, Byakuya assisted Makoto with finding evidence for the murder of Chihiro, though it was later revealed that it was used for Byakuya's entertainment and to help figure out who was a threat to Byakuya's plans, to which Byakuya identified Makoto as.

In Chapter 5, after Byakuya resolved to defeat the mastermind, he became less cold towards Makoto, such as being more willing to give him information and warning him about the dangers of protecting Kyoko during the fifth trial.

During the final class trial, Makoto helped rescue Byakuya from Junko's despair. Although Byakuya states he didn't need Makoto's encouragement, he was most likely lying.

In Danganronpa 2, Byakuya cooperated with Makoto's plan, agreeing to rescue the Remnants of Despair and Byakuya respected Makoto's decision.

In Danganronpa Another Episode, Byakuya says to Komaru, that she reminds him of Makoto when Byakuya first met Makoto, indicating Byakuya respects Makoto more after the events of Danganronpa.

In Danganronpa 3, Byakuya tells Makoto that he "was as tough as a cockroach, and as hard to kill," and that he wouldn't want them to be enemies. Aoi suggested that Byakuya was trying to make Makoto feel better, as the latter was thrown into another killing game.

Toko Fukawa
Makoto finds it difficult to talk to Toko, mostly because of her antisocial nature and the fact that Toko can be very accusative. Toko has expressed dislike for Makoto, saying she disapproves of him, but sometimes thinks of him as reliable. Makoto and Toko survive the Killing School Life together, and become members of the Future Foundation (although Toko is not an official member).

Yasuhiro Hagakure
A fellow survivor of the Killing School Life and member of the Future Foundation. Makoto is visibly the nicest to Yasuhiro out of all their fellow survivors, but often finds his eccentric personality confusing.

Leon Kuwata
During his free-time events, he shared a lot of things with Makoto and even invited him for a baseball match after they escaped the academy. However, it never came true as Leon was executed at the end of the first trial. Makoto himself didn't hold a grudge against Leon for killing Sayaka, because he felt that the one at fault was Monokuma.

Mondo Owada
Byakuya provoked Mondo to become enraged, Makoto tried to stop Mondo from doing something rash and ended up being punched by Mondo when trying to intervene. Mondo later apologized for his short-tempered actions showing he holds no disdain towards Makoto.

When Sayaka was murdered, Mondo assumed Makoto to be the killer due to the murder happening in his dorm room without considering other evidence, showing he did not fully trust Makoto by this point.

Mondo and Kiyotaka have an argument about who has the greater strength and challenge each other to an endurance contest in the sauna. Mondo requests Makoto to be their witness in order to have a fair contest showing that he now may trust Makoto more after the events of the first class trial in which his innocence was proved.

During Mondo's Free Time events he requested Makoto come riding with his gang after they escape Hope's Peak Academy. Makoto is unsure if it would be safe and Mondo stated Makoto could ride with him on his motorcycle, showing that he trusts Makoto and sees him as a close friend. Mondo also talks to Makoto exclusively about his indecisiveness over his career path, something that he stated he would share with no one else which presents the development of their friendship.

In Chihiro's final free time event, Makoto recommended Mondo as his trainer.

Makoto is able to discover Mondo to be the culprit of Chihiro's murder and upon hearing Mondo's reasons for killing Chihiro, Makoto started to feel guilty and was deeply upset when Mondo is sentenced to be executed.

Kiyotaka Ishimaru
Kiyotaka seems to regard Makoto in a friendly manner, or at least respectfully as a fellow classmate and student. In Kiyotaka's Free Time Events, their relationship deepens when Makoto manages to help Kiyotaka and his social skills with making friends, to which Kiyotaka responds by giving him the title of "Professor," much to Makoto's discomfort. Eventually, Kiyotaka comes to call Makoto a friend, and even entrust him with the knowledge of his grandfather, Toranosuke Ishimaru, and why he hates geniuses.

Sakura Ogami
Originally, Makoto was very afraid of Sakura, due to her reputation as a martial artist and imposing figure, but they eventually bonded during the killing game.

Sakura put a great deal of trust in Makoto, telling him about her past and her boyfriend Kenshiro. Makoto, in turn, told Sakura to be patient until they escaped and to embrace her femininity. Sakura stated that Makoto reminds her of Kenshiro in some ways.

Chihiro Fujisaki
Chihiro was good friends with Makoto and stated that talking to him made him feel better. Makoto, in turn, told Chihiro to become stronger and to feel better about himself. In a free-time event it is revealed that Makoto is partially responsible for Chihiro's death as he is the one who recommended that Chihiro train with Mondo to become stronger. Despite their closeness, Chihiro never told Makoto that he was a boy in the actual story. However, he does so in School Mode.

In Danganronpa V3 bonus mode Ultimate Talent Development Plan, during a Sports Festival Event, Makoto seeks out Chihiro to team up for a three-legged race because they are close in height. After finding and asking to team up, Makoto reassures a worried Chihiro that he is the only one he can count on to race.

Celestia Ludenberg
Celestia seemed to be rather fond of Makoto and she was curious to see if his luck as the Ultimate Lucky Student could beat her luck as the Ultimate Gambler.

During the Free Time Events, when Celestia does her personal ranking, she ranked Makoto with C-rank, which is higher than any of her classmates. While Makoto considers Celestia a friend, he is intimidated by her luck and that she would have a person assassinated if she found them boring which led Makoto to conclude that she is a friend that he needs to be careful with.

Hifumi Yamada
During their introductions, Makoto is made very uncomfortable by Hifumi's innuendos, despite that however, Hifumi seems to view Makoto in a friendly way, even finding him worthy enough to ramble about his interests such as Princess Piggles or his fanfiction creations.

Their relationship is deepened in Hifumi's Free Time Events and in School Mode, going as far as to call Makoto his "true friend" and even getting him to agree to join him as his apprentice/historian at his studio after they escape the school.

Mukuro Ikusaba
Before the Tragedy, Makoto was friends with Mukuro in Hope's Peak Academy Class 78th, though it seems they never became very close because of her distant personality. Makoto was the first person to ever smile at her, which led to her feeling a budding friendship for him. In Danganronpa Zero, she rescued him, claiming that she did it because they're classmates.

In Danganronpa IF, Makoto treated her very kindly and placed his trust in her, even after it was revealed that she was partly responsible for what had happened to Hope's Peak Academy.

Besides that, Makoto doesn't seem to see Mukuro the same way as the other Class 78th (after his memory was erased), as when he watched the brainwashing video she was not amongst the classmates that appeared before him. This could either be because he sees her, like Junko, as not a victim of the killing game, or because he simply cannot remember her image or personality due to his brain wash, and simply doesn't feel like she died in order to facilitate the eventual escape of himself and the other survivors.


 * Ultimate Despair:

Junko Enoshima
As the Ultimate Hope, Makoto was a major enemy of Junko. In turn, she seems to be one of the few people he genuinely dislikes, as he's usually very kind and forgiving. In turn, Junko thinks out of all the students in Class 78th, Makoto seems to be the most annoying and odd person in her class.

They developed a great hatred for each other during the Mutual Killing Game. In the end with the help of his friends, he had Junko Enoshima executed. However, even in her case, he felt that she didn't need to die and tried to reason with her when she was about to execute herself.

Though dead, Junko has found ways to antagonize Makoto through her AI form.

Besides his hatred for Junko, in Danganronpa IF, after he convinced Mukuro to think outside of Junko's world, he said that he would try to convince Junko in the same way as her sister, even after it's revealed that she's the mastermind of the Killing game.

Monokuma
During the Killing School Life, Makoto feels intense hatred for Monokuma, especially after the events of Chapter 1. The two maintain a fierce rivalry throughout the Hope's Peak Series, a battle between Hope and Despair. In Danganronpa 3 - Future Arc in the Final Killing Game, Monokuma states that this will be their final battle and conclude the history of each other between the last battle of Hope and Despair.


 * Reserve Course:

Hajime Hinata
Makoto put Izuru and the other Remnants of Despair in the Neo World Program. After waking up from the program, Izuru who successfully restored his previous identity, Hajime, brought his classmates to help Makoto to prevent Ryota from using his brainwashing video. Hajime is very thankful to Makoto, because of his hope his classmates return to their original personalities before being brainwashed by Junko.


 * Future Foundation Members:

Kyosuke Munakata
Makoto is Kyosuke's most persistent obstacle in his desire to eliminate Ultimate Despair. Because of Kyosuke's position as vice-leader, he was successfully able to charge Makoto with treason against Future Foundation and continues to antagonize him. Rather than just punishing him, Kyosuke is in favor of executing Makoto alongside the Remnants of Despair.

Contrary to what his actions might imply, Kyosuke admits to Makoto that he thinks he is impressive, and not just because he was responsible for the defeat of Junko Enoshima. Kyosuke respects Makoto's charisma and determination in the face of impossible odds; both qualities that were repeatedly displayed during the broadcast of the Killing School Life. Makoto implies that they had once been friends.

Despite this, Kyosuke is consistently at odds with Makoto because their viewpoints are so different. Makoto believes solely in hope, while Kyosuke believes in power. Because of this, Kyosuke thinks that Makoto's words are hollow and meaningless, as he does not appreciate despair in the same way that he appreciates hope. In his view, Makoto's experience with the Killing Games pales in comparison to the Future Foundation's battle in a world with no laws or restrictions on the depths to which the forces of Despair can sink in order to snuff out hope. Kyosuke also fears how influential Makoto can be, as he doesn't want him convincing people that they can win against despair without fighting.

Ultimately, Kyosuke's antagonism of Makoto is a clash of ideals on how best to reverse the damage wrought on the world by Ultimate Despair. Kyosuke also states that he'll eliminate despair at all cost, even if the despair itself was someone he dearly loved. However, Makoto managed to remind him to not forget about his beloved (In this case, Chisa) and Kyosuke began to change. He agreed to ally himself with Makoto, although he still seems somewhat wary of him despite Makoto trusting him completely.

Kazuo Tengan
Originally, Makoto had a great deal of respect towards Kazuo. He was thankful to Kazuo for defending him and blamed himself after he was murdered by Kyosuke. Makoto was shocked upon discovering Kazuo had been the mastermind behind the Final Killing Game, but didn't seem to hold a grudge against him or view Kazuo as an enemy.

Great Gozu
Great Gozu admires Makoto for his optimism in the face of adversity and has thought that way ever since seeing him broadcast in the Killing School Life for the first time. He sees Makoto as the type of hope that Future Foundation needs, and fiercely protected Makoto from Kyosuke for that reason.

Juzo Sakakura
Juzo has a strong hatred for Makoto and is often unable to look at or hear his name mentioned without showing disgust. His dislike was present long before Makoto had gone against protocol and sheltered the Remnants of Despair. In Danganronpa Gaiden: Killer Killer, Juzo is shown to hate Makoto so much that he requested the former Super High School Level Make-up Artist make a fake corpse in his image, which he used to infiltrate the Killing Festival and "murdered" in order to win over the crowd. When the Make-up Artist jokingly asked if Juzo was going to fight it, he answered that Makoto wasn't worth it.

Juzo despises the fact that Makoto is labeled a "hero," and mockingly refers to him as such. He doesn't believe that he deserves to be called a hero, after all of the lives his actions have directly or indirectly sacrificed. Additional reasons for his hatred include Makoto's conflicting ideals, and the trouble that Makoto has ultimately caused for Kyosuke. However, it was eventually discovered that Juzo hated Makoto due to the fact that he is able to stand up and defeat Junko, something that Juzo himself failed to do and blames himself on.

Juzo later saves brainwashed Makoto from suicide and confesses the reasons behind his hatred. Makoto tries to tell him that Kyosuke was tricked and that's why he attempted to kill him, and later convinces Kyosuke that Juzo still cares about him and he should go to him.

Ryota Mitarai
A fellow member of the Future Foundation. Ryota greatly admired and respected Makoto for his bravery during the Killing School Life, although the two don't share any close relationship in particular.

Bonus Mode Guides
The links below are a full transcript and in-depth guide for Makoto's routes in Ultimate Talent Development Plan and Danganronpa S: Ultimate Summer Camp.

Quotes

 * -|DR1=

Extra=


 * -|DRtA=


 * -|DRAE=


 * -|DR2=


 * -|DR3=


 * -|DRV3=


 * -|Novel=

Creation and development
From the planning stages it was decided that Makoto should not have much individuality, which made him difficult for character designer Rui Komatsuzaki to design compared to the other characters whose designs were more unique and distinct. Because the game was initially planned to be played from a third-person perspective from behind Makoto, he was designed wearing a hoodie with a distinctive decal on the hood to give players something to look at. His ahoge was added to give his hair some character, and he was deliberately made shorter than the other male characters in order to give him a ''-type image. His color scheme, though plain, were chosen because they were colors that Komatsuzaki particularly liked.

Trivia

 * Naegi means "seedlings" in Japanese, and Makoto means "faithfulness."
 * This could reference how he spreads hope to everyone, similar to how Junko tried to plant “seeds of despair.”
 * It was revealed that Makoto's full name is used as an anagram of Nagito's name. Nagito Komaeda is an anagram of "Naegi Makoto da" which means "I'm Makoto Naegi" in Japanese. According to Kodaka and Yoshinori Terasawa, the anagram was made as a hook to Danganronpa 1 fans due to the lack of promotion materials pre-release of the original version of Danganronpa 2 in 2012 . Kodaka wanted the fans to speculate that somehow Makoto and Nagito are connected in a way, and even cast the Japanese voice actress of Makoto, Megumi Ogata, to elaborate that idea even further.
 * In DISTRUST, he is not shown to have a name. Instead, 主人公 (Protagonist) is used as a placeholder.
 * The "gas mask symbol" on the back of his hood is a reference to "Zero" from the game, "". Another existing reference to "999" was mentioned by Makoto in the end of the fourth Class Trial.
 * Makoto is the one of the few characters to survive more than one killing game. The others are Aoi, Kyoko and Hajime/Izuru.
 * Byakuya and Makoto are the only characters to appear in every canon games and anime of the Hope's Peak Series.
 * In the first game, after being given the title "Ultimate Hope" near the end of the game, his e-Handbook profile lists his title as "Ultimate Despair." This is not a translation error, as it was the same way in the Japanese text.
 * In the non-canon Danganronpa V3 bonus mode, Ultimate Talent Development Plan, Celestia challenged him and Nagito to mahjong to test their luck. She then suggested they add the headmaster, Jin Kirigiri, to even things out. This is likely a reference to an official art from Danganronpa 1.2 Reload where the same event happened.
 * Makoto appears as a guest character in . His Max ATK is 7220 while his Max HP is 7380. His weapon is despair bat and its ability is doubled attack power. His deathblow is "Refuted", which causes small damage to all enemies within reach.
 * Makoto is also included in the collaboration of Danganronpa 3 x Hōkai Gakuen.


 * Makoto appears in Mystery Chronicle: One Way Heroics as the Ultimate Student class, being one of three designs available for it alongside Komaru and Monokuma.
 * The profile for the Ultimate Students states, You are the Ult. student. You may be the best, but you're just a student...You're not very good at close range combat. Master the various Truth Bullet (TB) skills and survive in this harsh world.
 * Makoto and Nagito share voice actors in both the Japanese and English dub. This is because Nagito's character is based on Makoto and he acts as his darker parallel.
 * Makoto is the only character to retain his original voice actor from the game for the English dub of Danganronpa anime adaptation.
 * Makoto and his sister Komaru (voiced by Megumi Ogata and Aya Uchida) perform Danganronpa Another Episode's ending theme Progressive -Zan Shin- together.
 * Makoto is one of the two characters to have a Rebuttal Showdown sprite and quote, but to never actually cause a rebuttal showdown, the other being Kokichi Oma.

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