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As this is a WMG, all spoilers will be unmarked ahead. You Have Been Warned!


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    Pre-Release & Mid-Let's Play 
The English-speaking audience's first exposure to this game was the Something Awful Let's Play. These are the theories proposed while the LP was ongoing.

Byakuya thought he was Framing the Guilty Party.
Contrary to his later claims, he didn't actually see the real murderer leave. He suspected somebody would snap thanks to the short time limit on Monokuma's "motives", however, and was discreetly looking around. When he discovered the body, he assumed that Genocide Jill was responsible, but was smart enough not to leave their obvious Calling Cards behind. Hence, he added those details in.

Then, to ensure they were correctly identified, he tapped the most obvious patsy, Makoto, whom had already proven himself easy to manipulate. He spoon fed clues to him so that he could safely pass that information on to the others without placing too much suspicion onto himself. That way, there'd be no chance of the 'stupid commoners' bungling the trial and letting a Serial Killer graduate. He didn't expect Makoto to Pull the Thread and realize he was responsible... or that he'd actually been fooled by Mondo, of all people...!

So why lie and claim he did it For the Evulz...? Better than admitting he'd gotten tunnel vision and not considered any other suspects than the one who'd literally fallen into his lap that same night. He'd rather come off as a Manipulative Bastard than admit he was wrong.

The goal of Despair Academy is to test one's resolution.
That is, the resolution to kill another human being. The photos that Monokuma snatches up after every other execution aren't just red herrings - they're actual pictures of the school building, of what's going on outside. The dead students are really just sent back to the "real world." The punishment for being too cowardly is to be stuck in your despair as things grow tenser.

The Monokumas are possessed by the spirit of a high school student who was dangerously envious.
Average in every respect, the boy (or maybe girl?) who would become Monokuma was jealous of every classmate who excelled in a certain field he/she could never thrive in. Torn apart by desire, proto-Monokuma eventually snapped and tried to murder an Ultimate student, but ended up being done in painfully by his/her own mediocrity. Now, he/she makes Ultimate students kill each other with utter delight, given supernatural powers from an unknown source.
  • "Average in every respect". So Monokuma is Makoto?
    • Probably not. Ultimate Lucky Student, remember?
  • Jossed.

Final Chapter survivor predictions
Assuming that there are two deaths per chapter, it means that there will be three people in the last chapter (Chapter 4 begins with seven people, removing one victim and one murderer drops to five. Chapter 5 would then remove one victim and one murderer, bringing the number down to three). Makoto has to be one of them due to being the main character. The other two would be "the victim" and "the rival", Makoto's opponent in the trial.

The rival would be either Kyoko or Byakuya, with the victim being the other one, or a Sacrificial Lamb that has survived throughout the game.

Now when Makoto and the rival discover the final victim's body, they stare at each other. A trial isn't called because there aren't three students who can witness the body. And then before anything happens Monokuma comes in. He doesn't like the idea of the graduating student being determined by who can kill the other first, so to create maximum despair he introduces his ace-in-the-hole: The sixteenth student. This count as the third student needed to identify the body, and the case begins.

In the final trial, Makoto and the rival plead their case before the sixteenth, who acts as the judge and jury. Monokuma announces that if the sixteenth pics the murderer, both the s/he and the innocent student are free to graduate (since it would just create a two-student scenario all over again). If the sixteenth pics wrongly, they both die instead and the murderer is free to go.

The reason "the rival" is not called "the murderer"? Because Unreliable Narrator may well rear it's ugly head, causing Makoto to be the murderer all along.

  • And Jossed thanks to chapter 4. D'oh!

Makoto Naegi really is super lucky, and not unlucky like he thinks he is
This possibility was brought up in the Something Awful thread by another poster, but it deserves repeating here. Makoto Naegi ends up getting the only dorm room whose bathroom door sometimes gets stuck...but because the door gets stuck, Makoto is later able to prove his innocence in a murder that was committed by someone who didn't know the true nature of the door.
  • Addendum: And then there's what happens to him at the end of chapter 3. Kyouko tells him of a secret room with files about the academy. When he investigates this room, someone bashes him on the head, knocking him out, and steals the files...but as an indirect result, Makoto ends up walking in on Sakura and Monokuma having a fight and that's how he discovers Sakura is Monokuma's mole.
  • Another addendum: And then there's what happens to him at the end of chapter 5, if you make the "correct choice" and choose not to reveal Kyoko's lie in court. This causes Monobear to unfairly cut the trial short, railroading the other students into voting Makoto as the culprit. This causes Makoto to almost get executed...but since Alter Ego saves Makoto at the last minute by dropping him down a trap door into the garbage room, and since Monokuma is now convinced Makoto will never make it out, Makoto essentially has free reign to explore the school however he wants, potentially solving the whole mystery!

Kyoko is Mukuro Ikusaba.

It's either a Memory Gambit, or the mastermind erased her memories for his/her/it's/their own purposes.

  • Jossed in Chapter 5, when Mukuro Ikusaba is confirmed to be the victim by Monokuma. Chapter 6 reveals that he wasn't lying about the identity of the corpse - the twist was that it had been a victim twice.

The evidence is building up to this. Especially with the massacre scene on the fifth floor.

  • The first part is confirmed by chapter 6, but the second part is still unknown.
    • The second part has essentially been Jossed by the two games that have come out since, plus the other supplementary installments.

Kyoko was framed by Monokuma/Mastermind/Mukuro Ikusaba.
Monokuma set up the crime scene in the 5th chapter to take out Kyoko once and for all, who's been snooping around. Mukuro Ikusaba is actually either Kyoko's true identity or the mastermind's identity. The corpse is actually one of Monokuma's earlier victims, Junko, placed in there to fool everyone. He set up the arrows in the locker to fool everyone into thinking the wounds caused by spears were arrows, plus the bomb on the corpse to prevent them from seeing its true identity.
  • As of Chapter 6, this is looking to be extremely likely.
  • Confirmed! There was no chapter 5 murder; the corpse is actually Mukuro Ikusaba, but she was killed in chapter 1 because she was masquerading as Junko Enoshima at the time. So Kyoko didn't do it, and it was in fact a frame-up as part of a trap Monokuma was setting for her. In the good ending Makoto gets caught in the trap instead, but is saved by Alter Ego.

    The Game 
After the events of Danganronpa, Makoto now has the abilities of all of the students of Class 78 combined.
Explanation time! In Super Danganronpa 2, Hajime Hinata is revealed to have also held the title Ultimate Hope. It is then explained that the Ultimate Hope was meant to be a superhuman jack of all trades. They could do anything with relative ease. In Danganronpa, as a result of completing free time events, Makoto learns different attributes from his classmates.

Meaning, by the end of the game, Makoto, in order, on top of his luck, has a detective's sharp analysis (Kyoko), has the artistry of a master fan fic creator (Hifumi), has a gambler's coyness (Celestia), has some level of clairvoyance (Yasuhiro), is a beyond expert swimmer (Aoi), has programming and computer literacy beyond compare (Chihiro), owns a strong moral compass (Kiyotaka), possesses a beautiful singing voice (Sayaka), owns a strike-out earning pitch and a home-run swing (Leon), has a vast knowledge and understanding of martial arts (Sakura), is a killer with the skill for twenty (Genocider), can create all the latest fashion trends and maintain them for years to come (Mukuro posing as Junko), and can even take over the Crazy Diamonds and lead it through The Worst, Most-Despair Inducing Incident in the History of Mankind (Mondo).

So, in short, Ultimate Despair is probably fucked.

In the bad ending, Toko isn't dead.
She's just taking the picture for everyone.
  • The fact that the only camera that we know was available to them lacked a timer would support this notion.

Toko grew up in a Chinatown situation.
One of her mothers is just the woman married to her father. The other mother is her biological mother (and sister).

  • Partially jossed. School Mode reveals that her parents just divorced and her father remarried.
  • Actually partially confirmed. One of her mothers is married to her father and the other is biological, but even she doesn't know which is which.

Celeste lied about her motive.
"Queen of Liars", after all. The whole "castle full of vampire-cosplaying manservants" thing? Just another lie. The fact of the matter was, she just didn't want to die quietly in a Gilded Cage — she wanted to be remembered. Pure and simple. And what better way to ensure that than to make up such an utterly outrageous lie? Especially since the others had been Sympathetic Murderers, making her stand out even more.
  • Or alternatively, Celeste has been broken with the 'motive' DVD so far and has become a Death Seeker, hiding her emotions. She went over the top with the motive because in her brokenness, she realized that she has been utterly horrible (whatever it is), so she made up a grand lie so everyone will think that she deserves to die for being a horrible person like that. She wanted a death fitting for a rotten person like that and think a simple death would not suffice.

Toko died from childbirth in the bad ending.
There's a blond-haired kid in the ending. She's more delicate than Aoi, and is extremely possessive of Byakuya.

The Worst, Most Despair-Inducing Incident in the History of Mankind was a form of subliminal brainwashing.
We haven't been told anything concrete about the Despairing Incident yet, but we have seen that its effects have caused the collapse of society. However, the mastermind has called Ultimate Despair a concept or idea, which has infected the entire world.

With this in mind, it's possible that the mastermind achieved this effect by broadcasting a subliminal Brown Note that killed the "hope" of everyone who witnessed it and turned them into sociopaths. This would also explain how the mastermind plans to destroy the remaining hope in the world by broadcasting the despair game; she's not just showing the last hope of the world killing each other, she's also broadcasting the same subliminal despair brainwashing that caused the Despairing Incident.

  • As of the release of Danganronpa 3... The theory is confirmed, at least partially.

The person Sakura needs to defeat is an unborn sibling.
After all, there's always the possibility someone could surpass her in the future.
  • Jossed. Her free-time segments explain that said person is her ex-boyfriend, Kenichirou. For worse, Sakura is soon dead... and it's all but stated that he is too, as he gave her the title of strongest martial artist because his days were already numbered.
  • Addendum: Turns out that Kenichirou is actually still alive as of Danganronpa Another Episode: Ultra Despair Girls. Given its placement in the timeline and the context of Sakura saying he had six months left, that means that he's lived about five times longer than he was given. He isn't the strongest in the world for nothing, apparently.

Genocide Jack is not Touko.
At some point in the two missing years, Byakuya, having access to the file on Jack and having already developed the theory that the hypothesized student behind that name would have to be drawn to Hope's Peak Academy, set out to find him/her, and for whatever reason settled on Touko as the most likely suspect. At the same time, she was developing a crush on him. When they met and he revealed the real reason behind his apparent interest in her, she snapped — and developed a secondary personality who could be the person he was seeking, so as to keep his interest. Byakuya then inadvertently fed her all the information about the real Genocider's crimes that she used to "prove" her identity. This explains the fact that he's still alive, and survives to appear in the sequel, despite her well-documented attraction to him, which would ordinarily make him a target for her supposed murderous tendencies.
  • Her What Could Have Been method of execution further supports this theory. Everyone dies in a way indicative of their personality — and her dominant trait is an obsession with Byakuya and a desire for his love and affection, not being a murderer with thousands of victims.
  • This is pretty unlikely given a few things. First off, the cuts on her leg to indicate her victims immediately become weird. Why are they even there if she's never actually had any victims? Genocider doing this wouldn't be something Byakuya would know about, so it'd be weird that she'd add that detail at all. Second, if this was true, where'd she get her scissors? We're meant to believe she's had them on her person since day one, but if she hasn't then where did she get them or how did she make them? It doesn't really add up. And let's not forget that in the final trial Genocider's memories pre-memory loss are used as evidence in the school trial. Sure she's pretty vague about them and could be lying, but if so it would be the first time the game is lying to us, since her memories are an evidence bullet. It just doesn't fit with how evidence has been handled in the game up until that point. As for Byakuya still being alive, we've yet to see exactly why that is (in the fan translated version, anyway, which is what I'm going by), but Byakuya is definitely smarter and probably more ruthless than Genocider's average victim, especially when you consider he knows that she's...who she is. All this would make it easier for him to avoid being killed by her. So while I guess this theory hasn't explicitly been Jossed, it's extremely unlikely considering everything we know.
  • There is another possibility - what if the real Genocide Jill is Toko's mother, not Toko herself? When she talks about her family and mentions having two mothers, it could be an allusion to her mother having a Split Personality like her. It would also explain how she got her hands on Jill's scissors, plus why she hasn't killed Byakuya (even with the two-year time gap). Hopefully when Toko/Jill's free time events get translated, we'll learn more about her background.
    • Unfortunately, Toko's free time events, and Genocider's, have both been translated, and they don't elaborate on that particular bit of strangeness. Most likely, it's simply explained by the fact that her parents are divorced — something you don't talk about in Japanese culture — and her father has remarried and given her a stepmother, who insists on Toko calling her 'mother'. (This has since been confirmed, see above.) However, Genocider's statement that she emerged because of "pressure society puts on us to be what society needs, not what we want", could still refer to Byakuya putting that pressure on Toko...
  • In the end this is Jossed, as Dangan Ronpa IF has her transform during what would be the events of the first chapter, before Byakuya even thought about Genocide Jill. Let the records show that I prefer this theory a lot more, though.
    • Most of what people are saying here doesn't actually Joss the theory; the idea is that Toko and Byakuya had an encounter during the year of their high school career, which they've both forgotten. If this is the case, then she would have already had her psychotic break by the time of the first chapter, facilitating that "transformation" and explaining where she got her scissors. Toko's scars could be self-mutilation — fairly common among emotionally unstable girls — that matched the number of Jill's victims when Byakuya made his initial accusation, which she subsequently kept up to match the number. Since Junko knew all sorts of embarrassing secrets about her classmates, she could have known that Toko was pretending to be a serial killer and allowed her to keep her scissors so that she might actually be cornered into killing someone. And the existence of Toko's alternate personality and that personality having memories of the Incident doesn't necessarily imply that that personality is completely honest about everything.
  • The parallels between the murders in the original game and Danganronpa 2: Goodbye Despair may also support this theory. We learn about Toko's split personality in the second murder. In the second game, the second murder involves a serial killer — but the actual serial killer is not present, instead someone is posing as a serial killer to advance a different goal.
    • Jossed. The second murder in the second game was committed by one of the students, Peko Pekoyama, with the reason being an old vendetta that goes back to the murder of Fuyuhiko's sister before The Worst, Most-Despair Inducing Incident in the History of Mankind. It has nothing to do with Jill.
  • Safe to say it's jossed as of Danganronpa Another Episode: Ultra Despair Girls

Toko/Genocide Jill was cured of her homicidal impulses during the two-year time gap
In Jill's free time events, she mentions that Byakuya is the first person she's fallen for who she hasn't had an urge to kill. Additionally, during the School Mode of the game, the same seems to apply to Makoto if you got Toko's ending, though you don't hear much from Jill there. With that in mind, it's possible that during the time gap, some Ultimate Psychologist or Neurologist gave Toko some sort of treatment that suppressed Jill's homicidal impulses, though it wasn't able to eliminate the Jill personality entirely.

In the mutual killing game, once Genocider is exposed, she plays up her serial killer status as a defense mechanism, so the other students are too afraid of her to try to kill her. Especially since she still has her memories and knows what happened on the outside.

We'll have to wait and see what further insights Another Episode gives us about her, since she'll be a central character there.

  • Sort of Jossed? In Another Episode, we see that Touko hasn't exactly made too much progress in ridding herself of Jill, and Jill is still a murderer. If anything the most we could say is that Toko has found an alternative to controlling Jill, but Jill is still kind of a problem for her.

In the demo version of the game where Yasuhiro was the first victim, Sayaka was the killer.
Like in the actual story, Makoto and Sayaka switched rooms, though Yasuhiro took the knife from the kitchen before Sayaka did. Despite this unexpected turn of events him over, Sayaka managed to slay Yasuhiro with his own knife, unlike very much the opposite happening as with the canonical situation where she invited Leon.

The Updated Re-release for the Vita will have expanded Free Time Events for some of the characters.
In the sequel, each character has at least five free time scenes, even the ones who die early. With the addition of the School Mode where you can play through free time events without anyone being murdered, it would make sense for everyone who doesn't already have at least five scenes to be given additional scenes. This could help to give some extra development to some of the early victims.

Of course, some scenes might not be available to the player on a first playthrough, particularly Junko (AKA Mukuro). This would be especially true if her new scenes ended up revealing her true identity before the player was supposed to figure it out.

  • Jossed. No new ones were added.

Junko Enoshima is still alive.
Given that she survived the first five executions apparently without a scratch, who is to say she couldn't have survived the last one, especially since there's a trap door right below her and the crusher.
  • Alternately: She meant to fake her death, but Alter Ego was still in the machine and made it squish her for real. Her expression when the crusher stalls is surprise that the trap door hasn't opened.
  • Let's Take a Third Option: suppose the door did open, except not all the way. Her body was crushed beyond repair, but not enough that the Remnants of Despair weren't able to salvage whatever was left. Picture then that there was a Frankenstein-esque 16th despair that didn't end up getting caught by the Future Foundation and sent to Jabberwock Island, with a talent allowing them to make off with her brain encased in a jar, to be revived later as a robot or something (ala Nekomaru, but for real). This hypothetical despair could have even been responsible for taking away so many specific memories by messing with the 14 students' brains (the precision with which Kyoko's memories of being a detective were removed suggests that only someone with an Ultimate talent could have pulled it off). This sets her up to appear one last time in the trilogy, less sane than ever: turns out she had a degree of awareness while being revived in the machines, and being left to her own thoughts was possibly the worst boredom she's yet felt. Which leads into an excellent final punishment everyone's favorite villain: being unplugged but kept alive, fully aware and unable to die.
  • Jossed. Danganronpa 2 confirms Junko died.

Byakuya is half-Caucasian, specifically French.
Byakuya's Free Times reveal that the head of the Togami family has multiple children with multiple women around the world, meaning that Byakuya is more than likely not full-blooded Japanese. Add to that his blonde hair in a universe where Japanese characters don't have blonde hair that isn't dyed, as well as the fact that he can speak French.
  • His DR:AE profile states he likes French cuisine.

Some of the gifts in the prize machine were originally owned by the students.
After all, it's likely they acquired more things over the regular school year before the Incident than the luggage they arrived with, and if they found something in with their stuff that they didn't remember having before, especially if it were something like a super-limited-edition T-shirt or a fancy radio, that might've raised questions too early. Waste not, want not.

Junko's personalities are all mockeries of the surviving students (sans Makoto.)
As detailed here.

  • Aoi: Cutesy personality
  • Byakuya: Haughty personality
  • Toko: Gloomy personality
  • Jill: Rude personality
  • Kyoko: Glasses personality
  • Yasuhiro: JoJo pose personality (this one's more dubious than the rest)

A thing to note: In the second game, one of Alter Ego!Junko's personalities acts almost EXACTLY like Genocide Jack. She has a faster and higher-pitched voice, acts hyperactive, and says "Kyahahahaha!" like Jack does.

Or alternatively....

Junko's personas are mockeries of those executed
This was an idea that popped in my head while thinking about the above WMG.

  • Cutesy is Alter Ego, because apparently it was so adorable Hifumi Yamada fell in love with it.
  • Haughty is Celeste, because she attempted to make herself seem queen/princess-like.
  • Rockstar is Leon, because he himself stated that he was sick of being a baseball player and wanted to become a rock star.
  • Glasses is still Kyoko, because of obvious reasons.
  • The persona that speaks in monotone is Makoto, because it's personality and voice are bland and monotone. What did Makoto describe his life as? Completely ordinary. Or, in other words, boring.
  • Sad is Mondo, because his backstory and overall effect of his trial was pretty depressing (or at least this troper thinks so)

And the Obligatory Warhammer 40,000 Theory Is...
Junko is the product of Nurgle and Slaanesh having a one night stand after the former took a swig of the latter's wine lake. The reason she remembers her home life being a war is because that's precisely what it was, they being Chaos Gods and all, and her unique strain of insanity is due to her desires for both Excess and Despair. Monokuma is a Malaite Demon Engine she roped into working for her, not that he really minds. The Most Despair Inducing Incident Ever was a repelled but still destructive invasion of Chaos, it being a lot weaker due to lack of grimdark, but Malal Cults are still running amok.

This also means that, due to Fate and Hope seeming to have a great affection for Makoto, his derailing of her plans in the Good Ending was part of Tzeentch's, since he metaphysically proved that the Changer of Ways is stronger than either Slaanesh or Nurgle. The "thank you" Daemon that inverts Monobear shows up after the epilogue and pledges his services, along with a few suggestions on how to spread hope by any means needed...

  • Bonus points: The Bad End was Tzeentch noticing his chosen prophet was about to screw everything up for reasons that would make perfect sense at the time, so he sent a vision of the future to stop him.

"Detention" wasn't Makoto's intended execution
The mastermind knows who committed each murder, so there's time to prepare the customized executions in advance. However, she prepared Kyoko's execution expecting that she would be voted as the culprit for the death of Mukuro Ikusaba, and when Makoto took the fall she didn't have time to set up his, so he got thrown into Kyoko's.
  • Confirmed. Kyoko gets this execution in the bad ending (where everything goes according to the mastermind's plan).

Hope's Peak operates on a Western school year schedule.

In the beginning of the game, the forum posts that Makoto looked at to get information about his fellow students are all dated August 20, 2010. Makoto says he accessed the posts the night before he arrived at Hope's Peak, and given the nature of 2ch-style forums it's unlikely that Makoto would be able to see these posts more than a few days after they were made. If this is the case, that would mean that he arrived at Hope's Peak around the end of August. This would explain why the Hope's Peak students were already enrolled in a high school when they were accepted into Hope's Peak - their high school had started in April, while Hope's Peak starts in September.

  • This is supported by the date of Makoto and Kyoko's execution. The blackboard laying out its name to the player ("Detention"/"After School Lesson") says it's happening on April the 1st, which makes it impossible for Junko to have organized the game during any timeframe that a Japanese curriculum would allow her.
  • Jossed by Danganronpa 3. Chisa is shown returning in March, and almost immediately after there's the entrance ceremony for the incoming class (Class 78). Her flashback to her graduation also shows the cherry blossom trees in bloom, which only happens in March. It looks like they do open in April like most Japanese schools. So Makoto's statement is probably a Retcon.

The unknown "speaker" of the tutorial text that explains new mechanics in the trials—

—is Jin Kirigiri, talking to Makoto from beyond the grave in a last-ditch attempt to aid the students. In conjunction with another theory somewhere on the site, Jin can only inform Makoto specifically because Makoto unintentionally gained some of Sayaka's esper powers when she went into his mind (meta reason being that Makoto is the PC)—and Makoto doesn't seem to be consciously aware of them. In theory Jin could also try to pass the information onto Yasuhiro, the Ultimate Clairvoyant, but Yasuhiro would've heard Jin on a conscious level and freaked the hell out.

Alternatively, the disembodied "voice" is Sayaka herself.

Makoto is the psychic in the class
Not only does he foresee the exact nature of Kyoko's execution when he's deciding whether to call her out, he gains the abilities of his classmates to use in trials when he spends enough time with them. That's not even considering School Mode, where he can literally read their minds.
  • Subverted. He just has good intuition.

If a murderer had successfully fooled the trial everyone would have died.
Monokuma would have killed all the others for choosing incorrectly, as threatened, but just as the murderer thinks they're home free they'd be slapped into their execution too as Monokuma reveals that even if they weren't found guilty they still failed at the rule about no other students realizing they did it. Junko knows they did. And pulling the rug out from under them at their moment of triumph would be the biggest despair kick she'd get in the whole game.

Taeko isn't actually rich
Because claiming she got fabulously wealthy purely from gambling earnings sounds perfectly in character for Celestia Ludenberg, but also like a story that a habitual liar would be willing to spin. Because of her age and Japanese gambling laws, she would mostly make enough to get by (groceries, living expenses, cat food) without much issue. Yet it was the fact that she could manage any kind of career as a professional gambler while still in high school that earned her the title.

It could explain why she always wears the same clothes in nearly every class photo: one could assume she just found a perfectly coordinated outfit and keeps several copies, but it's easier to believe that it's the only set of expensive Gothic lolita clothes she has, and she just takes very good care of them (since in her dream she's wearing a different set, which would probably be the first thing she'd buy with her 10 million). The fact that her curls are actually clip-ons could support this (taking care of hair like that would get expensive).

If Sayaka had lived longer...
She would have become the group's Living Lie Detector, as a counterpart to Celeste. The thing to remember about her title is that she isn't the Ultimate Singer or Performer, but the Ultimate Idol. And to survive in the world of Japanese pop (or music in general) requires some sharp business sense, a certain amount of deception against those who would exploit your weaknesses, and a keen intuition for reading people (hence her jokes about having ESP). To do so while still in highschool, where any other girl her age -no matter how talented they are- would probably get eaten alive, would require all these traits twice over. She admits to doing some unpleasant things to get where she is, and in the killing game, her BS detector could have probably been dangerously useful during the trials (perhaps more reason why she had to go).

Chihiro actually was transgender.
Canonically, Chihiro is male, and his story arc is set in motion by a desire to be more manly. Logically, since his memories were reset back to first entering the school, he would have had that desire during the lost year. Because most of the students were friends during the lost year, it also follows that Chihiro might have tried to act on that impulse during that time, too. However, every class photo shows Chihiro in the girls' outfit, as well as looking just as feminine as ever. If he had tried to become masculine through strength training, that would have carried over through the memory reset, and he might not have looked quite so feminine during the Mutual Killing game. It's far more likely that, because the class got along well, Chihiro was able to be convinced by Kiyotaka and/or Mondo that being one's true self is more important than being what you're expected to be. As a result, Chihiro likely came out of the closet during the lost year, and chose to retain a female appearance. Unfortunately (and tragically), this epiphany was lost when his/her memory was reset, and thus when the Mutual Killing game started, survival trumped authenticity, and he felt the need to become masculine, setting his fatal arc into motion.
  • Jossed. It's stated by Monokuma that Chihiro hated posing as a girl because it made his insecurities worse. He didn't like having to hide his real gender. Also, being told to be one's true self wouldn't convince Chihiro he's trans. It would convince him to stop pretending to be a girl when he's not. Furthermore, his desire to stop hiding the truth in the Mutual Killing was because his secret was about to come out and he wanted to accept him for who he was. He had no incentive prior to this as far as we know. Chihiro isn't transgender, end of story. The game spells it out that he isn't.

The primary reason Byakuya chose to unite against the mastermind with everyone else...
Was because Makoto and Kyoko solving a mystery that he couldn't made him truly realize that they're both better investigators than him. Confronted with this, he then had to acknowledge the fact that he wouldn't be able to create a mystery that they couldn't solve, rendering the "game" unwinnable to him. While he may have been legitimately inspired by Aoi and Sakura's actions, his line about promising to kill the mastermind was mostly an excuse intended to save face, like an emotional crutch that helps him accept someone else's superiority. This shows up again in the final trial, when Makoto saves him from despair; he knew at that moment that he needed Makoto's help, and brought it up as an explanation once more.

School Mode is the result of Junko pulling a Peggy Sue, hence why Monokuma talks about the Prologue and Chapter 5
This being Junko, she sabotages herself to get more despair.

Junko wanted to make Toko into Ultimate Despair
So think of this: in her last Free Time Event, Toko reads some of her poetry and manages to utterly depress Makoto with it (something not even Junko could pull off). So she's got the gloomy personality, and there aren't many things more despairing for the world than to see one its finest romance writers go evil. Having a serial killer personality would just be a bonus.

She then realized at some point that so long as Byakuya exists, both sides of her will always have a certain amount of hope, and Junko couldn't bring herself to merely kill Byakuya just to get an ally. She went through a lot of effort to wipe out the Togami conglomerate, in an attempt to show that even the most confident people can fall to despair; he absolutely must take part in her game for that reason. Hence, Byakuya saved Toko without realizing it.

There were originally more than sixteen students locked in the school
After all, Monokuma only says that no one has entered or left the school since the game began.

There's always been the question of how Junko and Mukuro managed to take over the school and set up the mutual killing game by themselves. They would have had to build all the Monokumas and control equipment, set up the trial room and execution deathtraps, and so forth.

Plus, there's only fifteen dorm rooms on the first floor, and sixteen confirmed students.

The easiest answer seems to be that the two masterminds didn't set everything up themselves; the Remnants of Despair were also locked in the school. Presumably, the second floor of the dormitory wasn't always in ruins, and had more housing for additional students. If Junko subverted half the students locked in the school, she would have been able to easily overpower the Headmaster and the students who refused to go along with her.

Afterward, it would have been easy for the Despair students (except for Junko and Mukuro) to escape, and for the remaining students' memories to be wiped.

Jossed: Danganronpa 3 confirms it was just the 16 students and Headmaster Kirigiri locked in the school. The Remnants faked their deaths during the Tragedy and then went out in the world to commit atrocities for Ultimate Despair.

The entire first game is Naegi's dying dream...

And he's actually the first murder victim (or was convicted for Sayaka's murder, resulting in the deaths of everyone but Leon as promised). There are a few pieces of evidence for this theory, including:

  • Makoto is the only one who has the whole "evidence bullet" thing, and the power to replay segments of discussion to pinpoint the fishy statement. Additionally, the investigation won't end until he's gathered all the evidence he needs, which could imply that he's subconsciously running things - creating a scenario that he can get at least some of his friends safely through like he never got the chance to do in reality. The fact that he, instead of Kyoko (the Ultimate Detective), is ultimately the one who convinces everyone of the culprit in each trial, is exactly the kind of thing a dying kid might come up with in order to come to terms with his death.
  • Whoever he talks to during Free Time, he will always end up close friends with that person by the end of the final conversation: he makes friends with people he still doesn't think he ever got a chance to know.
  • A more minor one, but in the ending song of the anime, he's shown with the deceased cast members up to that point despite not being deceased himself - or is he? It's possible these are the people whose deaths that occur after his death joining him in the afterlife, with Sayaka, Mukuro/Junko, or Leon being correctly convicted of his murder, and then one of the remaining two being killed by the other, who is subsequently caught. For the next two added, either Chihiro was killed by Mondo as in canon, or vice versa, or they were both killed one of Yamada or Ishimaru (the next two added) who was then caught. Then, either Yamada and Ishimaru's murders were orchestrated by Celeste as in canon, or she killed the one of them that hadn't been executed. After that, Sakura committed suicide as in canon, and then when the other characters join for the last couple of endings, it's because they convicted the wrong person (or indeed, anyone still alive) in that case and were killed slowly. In other words, the picture implies there were no survivors in the end.
  • Jossed: the subsequent games show him alive and well, so unless he's having a super-long dying dream, it's not possible.

All the students are in some way representations of Batman
Because, ya know... it's not hard to tie any number of characteristics to an already unrealistic 75-year old character.

Jin used to read Socki the Sock/Kutsushita Sokkusu-chan to Kyouko
So much that it became her favorite as a little girl. Not long after he abandoned the Kirigiri household, the book had begun to leave a bad taste in her mouth and now she despises it. Hence, digging around through a corpse's socks feels more personal to her than digging through their underpants; that feels like the best dramatic explanation for a one-note gag that never got explained.

Thanks to Junko, the bodies of the dead students are stored in the biology lab, exactly in the way they were. The Future Foundation entered the school after the Mutual Killing School Life, and they retrieved the bodies, and then they put them in the simulation, along with the six survivors, who agreed to have their memories erased.

The point? Revive the dead students. Since their bodies were kept untouched, it's possible that they could revive if they could restart brain activity. The plan is to recreate the students' personality based on the survivors' memories. The school, the place where they lived for a long time, was used because a familiar environment would be more effictive. All of their memories of dying, or other people dying, were cut, of course. When the time comes — namely, when the personalities are firm enough — they will be uploaded into the corpses along with an electric shock or something, which should have a chance of awakening them.

Mukuro Ikusaba once worked under the Haven Troopers.
Given the Haven Troopers' status as Elite Mooks and Doom Troops, and their greatly enhanced agility, it would make sense of the type of training someone like Mukuro would go through. Even if her abilities are not as grounded in reality as the Metal Gear universe (or at least, as grounded as Metal Gear can be).

Other Students' Dark Secrets

Because we never do learn any aside from the initial four.

  • Kyoko Kirigiri:
    • Has burns on her hands.
    • Is related to the Headmaster.
  • Byakuya Togami:
    • Guilty of insider trading or some other financial crime.
  • Kiyotaka Ishimaru:
    • Grandfather was a prime minister destroyed by a scandal. Yes, it isn't much and Kiyotaka tells Makoto during his free time events, but Kiyotaka was also willing to volunteer his dark secret and he's extremely conscious of family honor.
  • Leon Kuwata (if he'd survived to take part):
    • His cousin is obsessively in love with him.
  • Sayaka Maizono (again, prepared in case she survived):
    • Whatever "bad things" she said she had to do to make it as an idol, most likely sexual favors or dirty business tactics.
  • Hifumi Yamada:
    • Draws pornography of his favorite fandoms.
  • Yasuhiro Hagakure:
    • Is in debt to the mob.
  • Aoi Asahina:
    • Cheats on her diet.
  • Sakura Ogami:
    • Cheated in one of her matches.
    • Is the mole for Monokuma.
  • Celestia Ludenberg:
    • Is really Taeko Yasuhiro and her ringlets are fake.

Chihiro has an androgen insensitivity disorder

Chihiro has nearly nothing masculine about him — while this was probably just so that his sex would be a surprise, it doesn't really make much sense when you think about it. If he had gone through normal male puberty, he would at least have some sort of indicator of that. It would make sense if he had CAIS, a disorder that makes the body resistant to testosterone's effects despite having a Y chromosome.

The girl Hifumi yelled at in his backstory was Taeko, before she embraced her Celeste persona.

At the time, Taeko honestly wanted to try befriending Hifumi due to shared interests, only to be harshly rejected. She then saw this as a wake-up call to stop pursuing friendships and reinvent herself as a cold, closed-off loner, so that nobody will ever hurt her like that again.


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