Makoto Naegi

Makoto Naegi (苗木 誠 Naegi Makoto) is the main protagonist and sole playable character of Danganronpa: Trigger Happy Havoc and a participant in the Killing School Life and the Final Killing Game.

Makoto has the title of Ultimate Lucky Student (超高校級の「幸運」chō kōkō kyū no “kōun”), though he appears to have both bad and good luck. Later, his title became Ultimate Hope (超高校級の「希望」chō kōkō kyū no “kibō”), due to his unusual optimism and ability to spread hope.

Makoto survives the final trial and escapes Hope's Peak Academy with the other survivors.

Makoto returns in Danganronpa 2: Goodbye Despair and Danganronpa Another Episode: Ultra Despair Girls as a member of the Future Foundation.

The DVD/BD vol.1 of Danganronpa: The Animation came with a 25~ page booklet called ''Makoto Naegi’s Worst Day Ever. ''This short story describes the chain of events that led to Makoto being selected as the Ultimate Lucky Student.

Makoto also appears in Danganronpa/Zero and Danganronpa IF.

Makoto returns in Danganronpa 3: The End of Hope's Peak Academy - Side: Future, attending his trial after he was charged on suspicion of treason for protecting the Remnants of Despair.

During the Fianl Killing Game, Makoto unknowingly triggers Kyoko Kirigiri's NG code, which kills her.

Appearance
Makoto has a rather short and thin build. He has spiky, desaturated brown hair with a prominent ahoge, and washed-out hazel eyes. He wears a zipped-up dull green hoodie with a red stripe along the zipper, an open black jacket with gold buttons over the hoodie, black jeans, and red sneakers with white toes.

Makoto's hoodie has a logo 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 overlaid on a crescent moon; this is pinned to the lapel of his jacket.

After joining the Future Foundation, Makoto is seen wearing a black suit. He seems to have cut his hair, as it appears to be a bit shorter.

Personality
According to himself, Makoto is a very ordinary person, to the point that he feels a bit insecure about it. His most distinguishing feature is his unusual optimism.

Makoto is very kind, supportive and forgiving, though sometimes slightly naive. He is friendly, polite and a lot more down-to-earth than the other students. This is possibly the reason why he is capable of approaching and befriending them in Free Time sequences, even the most antisocial such as Byakuya Togami and Toko Fukawa.

Junko Enoshima refers to Makoto as a "herbivore man", which means that he is likely to be the passive one in a relationship; this is reinforced in his conversations with others. He is also a bit jumpy at times and quite easily pushed around by some other characters such as Byakuya. However, even though he is sometimes a bit of a pushover, he is also 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 the bad situation in the present. He is also a pacifist, as he believes that killing and 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 towards those who fell into despair, such as the Remnants of Despair, believing them to be victims of Junko Enoshima and not inherently evil.

The only person he genuinely dislikes appears to be Junko Enoshima, the True Ultimate Despair, and he considers her his enemy. 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.

Makoto is respected by many people as the Ultimate Hope, though he himself is very humble and even a bit embarrassed of 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 power to give hope for other people and affect their way of thinking. However, this is not always the case, as some people refuse to listen to him or simply do not accept his ideals.

History
[Warning: Several spoilers follow this section!]

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 was in the same class with Sayaka Maizono. 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 78th Class through winning a random lottery. The day before his first day at the Academy, August 20th, 2010, Makoto visited a forum and looked up information about his future classmates.

Makoto Naegi's Worst Day Ever
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 Jutaro 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 the long way home - he couldn't even wrap his head around everything. Correctly identifying Makoto as the cause of his recent misfortune, Jutaro 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. Jutaro 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 Jutaro, 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 Jutaro riding the motorcycle that once belonged to the postman. Jutaro threatened Makoto by saying that he'd hate him for the rest of his life if he ended up being arrested. Jutaro 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 a ordinary high school student.

At that moment, the motorcycle that Jutaro 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 Jutaro'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.

Chapter 3
During his first year at Hope's Peak Academy, Makoto bumped into Ryoko Otonashi in the medical bay while he was there to return the e-Handbook that Yasuke Matsuda had dropped.

Ryoko asks Makoto where Yasuke is and he answers he's probably out. Ryoko begins to rant in frustration and Makoto tries to comfort and calm her down. She is surprised by his notable kindness and finds him suspicious, thinking he's a pervert behind his nice demeanor. Both of them are confused by each other and Makoto seems to find Ryoko a bit familiar. He introduces himself and explains what he came to do. Though still a bit suspicious, Ryoko decides to believe him for now. Hesitantly, Makoto tells her that there's a rumor about 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 appears and grabs 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 Ikusaba 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 think he's lucky because Mukuro happened to pass by.

After an awkward silence, Mukuro notices someone's 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 Kirigiri 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 78th Class' school memories so they could participate in the school life of mutual killing.

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 titled "Orientation Info".

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 in a classroom 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, Monukuma 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 the very next morning. 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 overwhelming circumstantial evidence led Makoto to be blamed for the murder.

In Makoto's frantic quest to clear his name, he worked through numerous heated debates and collected evidence, eventually coming across conclusive proof that indicated Leon Kuwata might have been the one who killed Sayaka.

After Makoto arrived at the most logical conclusion of events that had transpired leading up to the murder, he had a brief but very intense debate with Leon. The latter was eventually found guilty of Sayaka's death, leading to Makoto's name being finally cleared from the murder. However, before anyone had a chance to fathom what was in store, Leon was then dragged off to his punishment by Monokuma.

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

Makoto would later learn from Kyoko that Sayaka's motive in writing her dying message could possibly have been to protect him, while regretting to have plotted for Makoto to be blamed for the murder. 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 blooded 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 Asahina 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 led 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 Ludenberg's scream, claiming that she was attacked by a suspicious figure known as “Robo Justice”. Celeste, 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 Taka'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 Celeste is the culprit of the murder. After saying the reasons why she killed their classmates, Makoto and the other students watch on as Celeste is executed.

Chapter 4 - All●Star●Apologies
After the 3rd Class Trial and Celeste'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 discover 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 find 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's 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 was 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
Prior to his miraculous 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 despair).

Kyoko then explains on his behalf that the trial was restarted due to some circumstances (basically thanks to Kyoko's 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, agree to stay in the academy during their interview with the former principal of Hope's Peak Academy, Jin Kirigiri; 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.

As the true perpetrator was revealed as the real Junko Enoshima, Makoto is surprised over reason behind Junko's sadistic survival game. During the course which almost all students were stunned over the truth; where details partially told by Genocide Jack (who knew the truth better than her other personality), only Makoto managed to analyze the course of event during his past journey in the academy, behind every offer and lure from Junko (mostly about based on despair):
 * 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 accidently kill Chihiro due to his uncontrolled rage and jealousy over Chihiro's inner strength.
 * Celeste's greed for the 10 billion yen so she can buy a European castle, including her fantasy about vampire butlers, would led her treachery to the group by killing both Taka 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 Hiro and Toko, as 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 Hiro that staying in the school, in this despair, isn't living at all. Hiro then realized that living means moving forward, even if it's hard and scary. So this rekindled his desire to leave this school and find his future.
 * He convinced Hina that they aren't just living for themselves, but also for their deceased friends. Hina then realized that Sakura, her deceased friend, would say that living means going against despair and walking through hardship. So this made her make up her mind.
 * He convinced Byakuya that the Togami Family never succumb 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. So this made him decide to keep his word and have the mastermind, Junko, defeated and dead (he also added that he isn't doing this for Makoto, though it is probably a lie).
 * In the game, Jack said to him that she doesn't care whether she stays here 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.
 * He convinced Kyoko that her father never gave up nor give in to despair and if there is no hope, then they'll become the new hope. Kyoko realized that her father would never sacrifice Makoto so he can stay and survive. This made her realize that even though they are related only by blood, doesn't mean she can not understand her father. She also realized and revealed that Makoto has the ability to defeat the Ultimate Despair, thus making him the Ultimate Hope.

With his classmates' solid support around him, Makoto managed to defeat Junko, leading her to execute herself in her very own special punishment (The Ultimate Punishment), which then resulted in her 'death', leaving the survivors finally free from the strings of the once sadistic game.

Epilogue - Goodbye Despair High School
Their torments finally over, Makoto then opens 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 Branch. 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 respond 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 became 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 led the students to choose the "graduation" so AI 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 AI 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 Academy - Side: Future
After returning from Jabberwock Island, Makoto has been charged with the crime of treason for protecting the Remnants of Despair. Everyone who gathered for Makoto's trial has been 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.

His NG code is "Not allowed to run in the hallway." However, it can be sidestepped by having other people carry him.

Episode 01 - Third Time's the Charm
Makoto arrived at the rooftop of Future Foundation's off-shore facility, where Kyoko, Hina, and Hiro 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 Sakakura to handcuffed him. Juzo sarcastically apologized to Makoto, saying that he's sad to have to do this to the great "hero" who brought down Junko Enoshima. When Makoto tried to respond, Juzo punched him in the stomach. He told Kyoko to shut up when she patronized him and said that none of them deserve 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.

Some time 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 the 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. Hina 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 Hina.

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, Hina 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 Hina. Miaya Gekkogahara later came to their side and showed them a safe place to hide. Gozu quickly leap 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, Hina, Miaya, and Great Gozu decided to barricade themselves in a room few minutes before the time limit hit. Makoto sit beside Hina and tried to comfort her not to worry again since they will always fighting despair together. Just before the sleep drug injected, Makoto wanted Hina to believe in his luck.

Makoto woke up sometimes later and found a trace of blood on his hands. When he looked at Hina, 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 Hina's body. However, it turned out that her death was faked by the attacker as he saw Hina 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 Hina took down his body and Hina 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 Hina 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 Hina, making Miaya referred them as her soul mates. When they heard someone was coming, Hina and Miaya created a diversion so that Makoto can safely reach the intercom room. He left the scene and hoped for their safety.

Reached the intercom room, Makoto announced via the speaker about Great Gozu's death and the motive behind his action to protect the Remnants of Despair. He believed that the Remnants of Despair were former students of Hope's Peak Academy that filled with hope until Junko Enoshima corrupted them into despair. He also explained about the Neo World Program, a program used to delete despairs inside them until AI Junko came and messed with the program. He told that he abandoned the game and wanted to talk with everyone in the intercome room. Furthermore, he also revealed his NG Code 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 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, Hina, 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 Hina prevented Miaya from volunteering herself to stop Juzo on 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 Hina encountered with Juzo after he successfully knocked out Miaya. Makoto told Hina 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 Towa, she could distract Juzo's attention and once again Makoto jumped to Hina'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 Hina 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 Hina 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, Hina 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 annalihated 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 Hina 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.

Execution

 * Main Article: After School Lesson

Alternate Execution
Makoto is put into a large barrel and Monokuma closes the lid. When he was about to escape, a sword came in from the exterior and grazes his face. While Makoto was shocked with fear, more and more swords are thrust into the barrel. The barrel is wobbling in the beginning, but after a number of swords, it stopped moving. Monokuma peeked into the barrel and closes it hastily. He runs away and the screen blacks out. This execution is only shown in the Official Fanbook.

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 Tradegy began, Makoto was seperated 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. He was a bit disappointed when she informs him that she would be staying in Towa City.

Makoto is once again conatacted 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.

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 Monokuma's motivational video in an attempt to motivate Makoto to kill. His parents' status is currently unknown.

Kyoko Kirigiri
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. This is coupled with other subtle hints that indicate that she has romantic feelings for him.

It is hinted in the novel, Danganronpa IF, that Makoto had a crush on Kyoko before their memories were erased, when Junko asked Mukuro if she had taken care of her rival in love, Kyoko.

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.

During the collaboration game of Danganronpa 3 and Guns Girl Z, Makoto blushes at one point as he mentions shyly that Kyoko looks cute. This surprises her and makes her blush as well.

Makoto ends up unintentionally killing Kyoko, as her NG code was allowing him to survive before the fourth time limit. Makoto was shocked and very much saddened by her 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.

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. Unfortunately, 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's Worst Day Ever, he enjoyed watching her performances after she became a pop sensation.

During the Killing School Trip, Sayaka recognized Makoto immediately and befriended him. A mutual attraction formed between the two and she even considered herself to be his "sidekick". 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 of her absence, Makoto goes looking for her worried about the condition she was in. Upon finding her dead in his bathroom, he was devastates, 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 one last time, 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.

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.

Mukuro Ikusaba
Before the Tragedy, Makoto was very good friends with Mukuro in high school. He was the first person to ever smile at her, which led to her falling in love with him, although he seems to be unaware of this. 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.

Aoi Asahina
Although not sharing any kind of close relationship with Hina 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, Hina requests that Makoto act as her fake boyfriend so she can practice when she gets a real one. Their closeness is also shown when Hina is shown feeling guilty over having executed Makoto and she seems happy when he forgives her.

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

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 realised they were worlds apart, but began to understand him.

During Chapter 2, Byakuya assisted Makoto with finding evidence for the murder of Chihiro Fujisaki, 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 to 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 Asahina suggested that Byakuya was trying to make Makoto feel better, as the latter was thrown into another killing game.

Quotes

 * “Being able to touch a body without any reserve… I don't think I’ll ever be able to get used to it, no matter how many times I have to do it...”
 * “Are you sure you aren’t telling me just because I don't have your trust…?”
 * “No, I'll definitely figure it out...!”
 * “What the hell are you saying...! This is all your fault...!” (to Monokuma)
 * “NO, THAT'S WRONG!”
 * “I'VE GOT IT!”
 * “NOW I UNDERSTAND!”
 * “HERE'S MY ANSWER!”
 * “THIS SHOULD PROVE IT!”
 * “THE KILLER IS... YOU!”
 * “HERE'S EXACTLY WHAT HAPPENED!”
 * “You want to see the bodies? That doesn't sound like something a lady would say.”
 * “After all, my only redeeming quality is my optimism.”
 * “Then promise me something. If at any point you think it will become dangerous, just let it go.”
 * “You're wrong! I believe in you, Kyoko! That's why I want you to trust me too.” (to Kyoko Kirigiri)
 * “DON'T LOSE HOPE NOW!”
 * “HOPE KEEPS GOING!”
 * “She doesn't yearn for any kind of future at all... She fills every person she meets with despair!” (talking about Junko Enoshima)
 * “What I believe is not their past, but their futures!”
 * “At least...this wasn't the ending prepared for them. This was...the ending they created.” (talking about the Remnants of Despair)
 * “Even if there's the smallest possibility... They're still trying to create that future for themselves... In their eyes, that is the future.”
 * “They've accepted their hopes and their despair, and they're trying to create their own future... Maybe, for people like that, miracles and inevitable, don't you think?” (talking about the Remnants of Despair)
 * “We...must create our own futures, too.”
 * “R-Really? Well, being positive is like... my only good point.” (to Komaru Naegi)

Creation and development
Right from the start, Makoto was designed to be a "protagonist lacking much individuality". According to the character designer, Rui Komatsuzaki, this made him much more difficult to design when compared to the other distinctive characters.

At first, the adventure part of the game was intended to be seen from a third-person camera, so the protagonist was given an interesting-looking hoodie that would be nice for the player to look at.

After that, the ahoge was added to give some character to Makoto's hair. His herbivore nature was highlighted by giving him a short stature.

He was given a subdued color palette, a one Rui Komatsuzaki especially likes.

Trivia

 * Makoto's report card in Danganronpa Another Episode states that:
 * He likes curry and trendy things and that he dislikes dried pickled horse mackerel and dried tofu.
 * Makoto's hobbies include watching TV and playing video games.
 * In Chapter 2, it was mentioned that he wet his bed until 5th grade.
 * 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”.
 * According to Makoto Naegi's Worst Day Ever, it is revealed that Makoto wasn't the first chosen for his year to be Ultimate Lucky Student, but rather events pertaining to his bad luck led to another draw occurring.
 * The official reload artbook reveals that A Man's Fantasy is his favorite free time present. A Man's Fantasy is an Easter egg present which allows Makoto and the other male cast members to peek at the girls taking a bath.05-22.jpg*Due to an error 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".
 * Makoto and Nagito Komaeda share voice actors both in 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's anime adaptation.
 * The "gas mask symbol" on the back of his hood has some meanings:
 * It represents protection, referring to how he did not get killed and how Alter Ego saved him from his execution.
 * It acts like a reference to "Zero" from the game, "999". Another existing reference to "999" was mentioned by Makoto in the end of the 4th Class Trial.
 * Makoto and his sister Komaru (voiced by Megumi Ogata and Aya Uchida) perform Danganronpa Another Episode's ending theme Progressive -zenshin- together.makotogunsgirlsz.png
 * Makoto appears as a guest character in Chain Chronicle: Brave New Continent. 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 and Guns Girl Z.