Makoto Naegi introduces us to Hope's Peak Academy, a special school that accepts only students who excel at their personal fields, as scouted out by the school itself. These students are then called Super High School Level/Ultimate [Talent] (the former in the Japanese verison, the latter in the official English translation). Makoto himself is the Ultimate Lucky Student, being a completely normal teenager chosen by lottery to join Hope's Peak.
But before he can actually do anything, he blacks out and awakens alone in a classroom. The windows have been covered by steel plates, and after wandering around for a while, he finds himself in the entrance hall, which has been even more drastically changed, with the doors being replaced by a large steel portal, sealed shut. Here, he also meets his classmates:
Aoi Asahina, the bubbly Ultimate Swimmer, Byakuya Togami, the haughty Ultimate Affluent Progeny, Celestia Ludenberg, the Elegant Gothic Lolita Ultimate Gambler, Chihiro Fujisaki, the tiny and nervous Ultimate Programmer, Hifumi Yamada, the Ultimate Otaku/Fanfic Creator, Junko Enoshima, the Ultimate Gyaru/Fashionista, Kiyotaka Ishimaru, the hardass Ultimate Prefect/Moral Compass, Kyoko Kirigiri, who doesn't even bother telling you her talent, Leon Kuwata, the Ultimate Baseball Star (who doesn't care for baseball despite his natural talent and wants to be a musician), Mondo Owada, the Hot-Blooded Ultimate Biker Gang Leader, Sakura Ogami, the Ultimate Martial Artist (and a woman despite her masculine appearance), Sayaka Maizono, the Ultimate Idol/Pop Sensation, Toko Fukawa, the prickly Ultimate Writer, and Yashuhiro Hagakure, the Ultimate Clairvoyant (who boasts a 20-30% accuracy rating).
Sayaka recognizes Makoto; they went to the same middle school, and although they weren't close, she remembered an incident where he rescued a crane (the bird). She appoints herself his sidekick, but before any sides can be properly kicked, Monokuma shows up.
Monokuma is a strange half-white-half-black plush bear, and identifies himself as the academy's headmaster. He gives the students an ultimatum: If they can get away with murder, they graduate. If not, they'll stay in the school building (which is self-sufficient) for the rest of their lives.
And with that, he leaves them to freak out.
Makoto and Sayaka explore the school's first floor together (there's shutters blocking the stairs up), and talk. But the cute bonding (with some hints that Sayaka might be a little traumatized by her idol career) is interrupted by Monokuma. None of the students are actually inclined to just up and murder someone- even Togami, who openly does want to play the game, wants to scout out his opposition first. So he announces that he has prepared a motive for them, and hands everyone videos to watch alone.
Makoto's video is of his parents and his little sister Komaru happily sending him off to Hope's Peak- only to cut to their empty couch and destroyed living room, with the ominous message that he'd only find out their fates after graduating. Everyone else is freaked out by their motive videos, but none more than Sayaka, who runs out of the room in a panic. Makoto follows her and is able to calm her down somewhat with a Declaration of Protection, but the poor girl is still rattled. To help her with her fear, Makoto finds her a gilded practice sword she can defend herself with, and the two swap rooms for the night.
... And of course, Sayaka turns up murdered in Makoto's shower the next day, with a knife in her stomach and 11037 written next to her in blood. So much for the protection. Makoto is the prime suspect, which is especially worrying as Monokuma declares that after every murder, the class will hold a trial, and if the true culprit (the 'Blackened') is found, they will be executed. If not, everyone but the Blackened will die. And to prove he's being serious about the execution thing, he kills Junko for supposedly attacking him.
Thankfully, in the class trial, Makoto is able to clear his name with the aid of Kyoko Kirigiri and a few pieces of evidence- for example, his shower door sticks closed and the culprit broke in because they thought it was locked, but Makoto knew the trick to opening it. With that out of the way, they move to figuring out the true Blackened, with a lot of trouble because the killer didn't actually plan on killing anyone; Sayaka did.
You remember how Sayaka was seriously affected by her motive video, which insinuated her idol friends were dead? Yeah, she wasn't really calmed down. She plotted to graduate by using Makoto as a patsy and Frame-Up target. She invited someone to Makoto's room (where she was staying the night), and attacked them with a knife she took from the kitchen. However, that someone used the practice sword to defend themselves and broke Sayaka's wrist, causing her to drop the knife. She then fled into the shower, and the person she'd thought to make her victim broke in and killed her with the knife she'd meant to use on them, with her last moments being used to leave a final clue.
And who is her killer? Someone that English-speaking fans knew was the culprit ever since they first saw '11037': Leon Kuwata. '11037' wasn't actually a number, it was Leon's name, written upside-down, backwards, and in English. The Japanese cast, with the exception of Kyoko, mistook it for Arabic numerals due to their unfamiliarity with English. Leon took advantage of the opportunity to murder Sayaka (and it was murder, because he could have left after breaking her wrist, but instead broke into the shower room), and used his talents as the Ultimate Baseball Star to dispose of evidence in the incinerator despite there being a fence blocking access to it.
Leon is then executed by being stoned to death with baseballs. Kyoko offers Makoto some consolation about his friend's attempted framing of him by telling him that Sayaka was probably extremely conflicted about her plan; she was driven to kill in desperation and Leon was able to fight back because of her hesitation. Kyoko theorizes that she left her dying message to posthumously exonerate Makoto, though Makoto theorizes she did it to take revenge on Leon.
Well, she's dead and now no one will ever know the truth. Oops.
Monokuma has a new motive for the class: Dark Secrets. He has a file for each student containing an embarrassing secret, and if there's no murder in the next 24 hours, he'll reveal all of them. Makoto really doesn't have much to fear; he's so normal that the worst Monokuma could find on him was that he wet the bed until 5th grade. Hardly murder material. But given his classmates' backgrounds, it's likely that not all of them have such mundane secrets.
On the bright side, the second floor is open now as a reward for passing the first Class Trial. It has a pool and changing rooms full of exercise equipment, much to the delight of class athletes Aoi and Sakura. There's also a sauna, which becomes relevant when Mondo and Kiyotaka have a disagreement and agree to settle it with a sauna endurance contest, with Makoto as a referee. Makoto ends up going to bed in the middle of it, but come the next morning, Mondo and Kiyotaka have become best friends somehow. Don't question it.
Sadly, this doesn't last, as Chihiro Fujisaki is murdered, found dead in the women's changing room, crucified and with 'BLOODBATH FEVER' (or 'BLOOD LUST' in English) written on the wall. Aw, nuts. Byakuya thinks it's the work of the Serial Killer Genocide Jack (Genocider Sho in Japanese), and ropes Makoto into the investigation.
During the Class Trial, a few interesting things come to light. First, Genocide Jack is amongst the students. She is Toko Fukawa's split personality/dark secret, a fact she revealed to Byakuya due to her obsessive crush on him. Second of all, Jack didn't do it. The murder scene was only an approximation of Jack's normal modus operandi, and she's actually resolved to not kill at all during the Killing Game (she doesn't want to kill anyone except in her usual way, and she's pragmatic enough to realize that her usual shtick is a great way to get herself caught). Byakuya just tampered with the crime scene, to learn more about the competition. Naturally, this wins him no friends, but he doesn't care.
Byakuya's smug facade breaks when Kyoko and Makoto reveal a fact about the crime scene he genuinely didn't know; that it was moved. The crime did not take place in the girls' changing room, but the boys' room. And the reason for that? Chihiro was a boy. That was his dark secret; he was a boy In Touch with His Feminine Side who was always bullied for being weak, so he started crossdressing so that he wouldn't be bullied for being girly. He'd wanted to start working out to become strong for when Monokuma inevitably revealed his secret, but that didn't work out as he was murdered there by his exercising buddy.
But who was said exercise buddy? That's up in the air until Mondo Owada slips up. He mentions that Chihiro wore a blue tracksuit- something Celestia saw, but the color was something she only told Makoto, and by her testimony the only way someone could know Chihiro had a blue tracksuit was by seeing him wear it in the changing room... and it was already established that the person there with him was the murderer.
Once cornered, Mondo breaks down and admits to the crime. He didn't actually mean to kill Chihiro, but he was in a very bad mental state due to Monokuma's motive. His Dark Secret was that he was involved in his brother Daiya's death; he challenged his brother to a race and almost got hit by a truck, but Daiya pushed him out of the way and took the blow instead. For the sake of his gang, the Crazy Diamonds, Mondo always pretended that he'd won fair and square and Daiya's death was an accident, and he feared that with the secret out, they'd break up. Chihiro just happened to press his Berserk Button at the worst possible time by calling him strong (while Mondo in turn thought Chihiro was the strong one for being willing to take having his secret revealed, while Mondo was afraid of the same), causing Mondo to black out and kill him with a dumbbell. He then moved the crime scene in order to keep Chihiro's secret, since it would've come out at the start of the investigation if Chihiro had been in the boys' locker room.
Mondo accepts his impending execution with grace, but Kiyotaka doesn't. Mondo was the first friend the poor guy ever had, and he desperately defends his friend and begs Monokuma to spare him, but it doesn't work. Mondo is tied to a motorcycle in a bike cage that runs so fast the friction and g-forces quite literally melt him. The chapter ends on a low note as Makoto notices how the remaining students distrust each other.
A new floor has been unlocked, with art rooms, a science lab, and a rec room, but poor Kiyotaka isn't in any state to appreciate it, being in a deep Heroic BSoD ever since Mondo's execution. Monokuma gives the students a new motive: money ($10M dollars, or 10B yen). Hey, he's gotta come up with a lot of motives, not all of them can be winners (though Byakuya thinks it's too little money for him).
Meanwhile, Aoi sees what she thinks is Chihiro's ghost in the changing rooms. It's actually a laptop with a special program Chihiro made: Alter Ego, an AI that takes Chihiro's face (though it can also imitate Mondo to give Kiyotaka a pep talk). The students' outlook brightens as they realize Chihiro has left them a potential weapon that Monokuma doesn't know about (there aren't any cameras in the changing room), and both Hifumi and Kiyotaka take quite a shine to the AI, though for different reasons. Hifumi, with his love for 2-d, has a crush on Alter Ego, while Kiyotaka sees him as a Replacement Goldfish for Mondo (even after he takes on part of Mondo's personality/channels his spirit to become Kiyondo). Kyoko promptly bans both of them from going near the AI without proper escort.
The class's search for the AI is cut off when they have to rush to Celestia, who's been attacked by an unknown figure in a 'Justice Robo' costume, using a small hammer labelled 'Justice Hammer #1'. The students run around trying to find Justice Robo guy, finding an injured Hifumi (plus Justice Hammer #2, which is slightly bigger), and then Kiyotaka's corpse in the science lab, killed by Justice Hammer #3. Then Hifumi is killed in the infirmary by Justice Hammer #4, and his corpse later disappears along with Kiyotaka's and is found in a storage room. Justice Robo is finally found stuck in a locker, and it's ... Yasuhiro Hagakure? The Ditz? Really?
If you smell a rat, you are not alone. In the class trial, the evidence against Hagakure is swiftly disproven (the Justice Robo costume was too clunky to properly move in, for one), and then the timeline of events comes under fire. The whole thing was an elaborate setup to make it look like a single culprit was running around, slowly increasing hammer sizes, and killing people while the search was ongoing. In reality, Kiyotaka was killed before any of the other things happened, and Hifumi was only pretending to be injured and dead the first two times. He was really dead when found in the storage room, because his partner-in-crime killed him to cover up loose ends. So, who's the mastermind of this overcomplicated plot and the true Blackened of the chapter?
Well, who's been the only one to supposedly see 'Justice Robo', who directed basically every step of the operation, and has been suspiciously insistent about Yasuhiro's guilt even when it was seemingly proven that he didn't do it? Celestia Ludenberg, the Queen of Liars, who was desperate to escape the school, with the monetary incentive being her final straw. She provoked Hifumi to kill Kiyotaka and participate in her plan by telling him Kiyotaka raped her and stole Alter Ego (which Hifumi was inclined to believe because of their rivalry), and said that she'd kill some other random person for her own escape. Hifumi, being Super Gullible, believed her even as her plan put him in the perfect spot to be killed for real.
Celestia (who reveals that her real name is Taeko Yasuhiro) takes her execution with probably-faked grace, and gives the other students the key to the locker she stashed Alter Ego in (she didn't even move it from the changing room). She is set up to be burned alive, but Monokuma interrupts that by throwing a fire truck at her.
With Celestia gone, most of the remaining students are the ones who are very unlikely to commit murder (And Togami). Kyoko shows Makoto a secret room hidden behind the men's bathroom, but Makoto doesn't have much time to investigate as a mysterious person wearing a luchador mask and a labcoat knocks him out and steals everything in the room. Oh well.
That night, Makoto sees Sakura fighting Monokuma in the gym, but keeps this fact to himself (pissing off Kyoko in the process), as he doesn't know the context and doesn't want suspicion to fall on her. Unfortunately for him, Monokuma shoots that out of the water by declaring that Sakura is The Mole amongst the class.
Aoi Asahina, being Sakura's best friend, wants to trust her and believes that Monokuma outright saying she's the mole means Sakura is of no more use to him, and that distrusting her is playing right into the bear's hands. Togami, on the other hand, takes the revelation as an excuse to treat Sakura as a pariah, and poor Makoto is stuck in the middle. Tempers rise and Genocide Jack injures Aoi, but before anything really bad can happen, Sakura shows up, dead in the rec room.
This case is a Locked Room Mystery, as the door was jammed shut and the window had to be broken to open it. Toko and Yasuhiro make themselves suspicious, but it eventually turns out that, while they were in the room before Sakura's death, they also left the room beforehand. Evidence eventually points to Sakura being poisoned, and the culprit seems to be... Aoi!?
Byakuya is happy to believe that Aoi was faking her friendship to Sakura and took the opportunity to poison Sakura's protein powder, but Makoto is more suspicious and discovers that Sakura had committed suicide, and Aoi faked being the culprit by switching her protein powder with the poison Sakura used. She wanted suspicion to fall on her, she wanted herself to be voted guilty despite being innocent, and she wanted the whole class to die with her.
Why? Because of Sakura's suicide note, which said that she had crossed the Despair Event Horizon because of her classmates' mistreatment of her. Aoi felt that they all caused her best friend's death, and that none of them deserved to live. Of course, this doesn't work and Sakura is instead found guilty of her own murder.
Monokuma then decides to twist the knife by revealing that the sucide note Aoi read was a fake; the real one stated that Sakura had become a mole because Monokuma had held her family dojo hostage and blackmailed her to commit a murder if no one else did (the only reason she wasn't the Chapter 1 culprit is because Sayaka snapped first), but that she regretted it after befriending her fellow students. She committed suicide because she knew that tensions would continue to rise after she'd been outed as long as she was alive. Monokuma said she had to kill someone to keep the Dojo (and possibly human hostages with it) alive, so she decided she was going to kill herself. The blocked door was so that nobody else could be considered a suspect and nobody would be executed, and Sakura finishes the note by begging Aoi to live for her, and telling Monokuma she'll get her revenge posthumously.
Monokuma thinks that this reveal will get the class to turn against Aoi for trying to get them all killed All for Nothing, but Makoto has other ideas. He tells Monokuma off by saying that this isn't a fair judgement of Aoi, who only tried this because Monokuma faked a suicide note. Aoi was only doing this because Monokuma manipulated her, and Makoto, followed by his fellow survivors, forgives her for it.
In fact, the revelation of Sakura's true suicide note has the exact opposite effect, as the students rally behind Makoto and Aoi against Monokuma. Even Byakuya declares that he will no longer play the game, because Sakura's selflessness has driven the game off the rails and because he's realized that he has no fair chance of victory if Monokuma is willing to tamper with crime scenes.
Monokuma gets a consolation prize by executing Alter Ego for hacking into the school network.
Now the Mastermind of the Killing Game is getting desperate. The class is united against them. Nobody is biting at any of their motives. Sakura's final act of vengeance was breaking the lock on the door to the Headmaster's Office, allowing Kyoko to get in and snatch a few goodies: a student profile for the mysterious 16th Student, Mukuro Ikusaba, and a master key that allows her access to any room.
So, the Mastermind tries something new. The masked and labcoated person tries to kill Makoto, but Kyoko saves him. Then, the masked person, who Monokuma identifies as Mukuro, is found dead in the 5th floor garden (and blown up with a bomb before anyone could get a closer look), and the only people without alibis are Kyoko and Makoto. The other students were together disassembling a Monokuma robot all night. And during the investigation, Makoto discovers that the Killing Game is being broadcast to the world.
The trial goes back and forth as Kyoko attempts to defend herself and cast suspicion on Makoto, but it all comes down to one moment. Kyoko's alibi depends on her not having the key to her room (Byakuya confiscated it), but Makoto knows she has the master key and could enter anyway. Does he call her out, or not?
If he does, then game over. Kyoko is executed by a giant crusher, and with her gone, nobody has the skill nor resources to investigate the school any more. No more killings occur, but the students have no way to unmask the Mastermind nor escape the school. They live there together (except Toko, who apparently died in the interim), and Aoi has everyone's babies.
If Makoto chooses not to call her out, then suspicion falls on him, and he's executed in the same way. But unlike Kyoko, it doesn't take. Alter Ego's hack was more successful than Monokuma thought, and he intervenes and halts the execution, sending Makoto falling into the garbage dump. He's smelly, but alive.
Kyoko comes to save him, being regretful of throwing him under the bus for her own benefit. She explains that neither of them were guilty of killing Mukuro; it was a frame job by the Mastermind as Kyoko was getting too close to the real secrets of the school. This is a good sign, because the Mastermind interfering means the game is slipping from their control. Kyoko uses her master key to get Makoto out of the garbage room, and while climbing a ladder back to the school proper, reveals some of her past (which she couldn't say earlier because the Mastermind erased her memories): that she is the Ultimate Detective and the headmaster's daughter. She resents her father for abandoning her, and came to Hope's Peak to announce that she's cutting all ties.
Once in the school, Kyoko confronts Monokuma. She convinces him to do a retrial because the Mastermind broke the rules by allowing the innocent Makoto to be executed, and breaking the rules would mean that the audience in the outside world wouldn't see a harsh game of students breaking and killing each other, just some random all-powerful jackass trapping and killing a bunch of students. Monokuma sees her point, and acquiesces. The final trial will be to discover all the secrets of the school, and all of the school will be open for the investigation.
During the investigation, Kyoko found out that her father truly cared for her... and also that he's dead, being the guy reduced to bones in the cold open. She takes a break to deal with this, while Makoto continues the investigation and finds signs that the students hadn't been immediately kidnapped for the killing game, but had spent some time as students at Hope's Peak... and that they had agreed to lock themselves in the school.
In the trial, Makoto proves that nobody killed Mukuro Ikusaba back in chapter 5... because Mukuro had died long before chapter 5. Her dead body was just used to fake the murder. She was actually killed way back in chapter 1, but the students didn't realize it at the time... because she was disguised as Junko Enoshima. The real Junko was not only alive, she was the mastermind.
Junko herself then proceeds to confront the survivors. She explains a few things, such as Mukuro being her fraternal twin sister who was in on her plot, and how she is the Ultimate Despair because of her fetish for both feeling and spreading despair (get used to hearing that word a lot). She killed Mukuro partially because she didn't think Mukuro could convincingly fake being Junko for the whole game, and partially because it's so despair-inducing to have one's beloved sister die by one's own hands.
Junko then confirms Makoto's suspicions that the students knew each other before the Killing Game; they had spent one year as students and one year staying in the fortified academy, but Junko erased those memories. And as for why they wanted to trap themselves in Hope's Peak, even though they all wanted to escape in-game? It's because Hope's Peak is a paradise compared to what Junko has done to the outside world. She has spread her despair to the entire world, creating a Monokuma-themed dystopia.
Junko then gives the students a Sadistic Choice: Either they choose Hope (embodied by Makoto), or Despair (embodied by her). If they all choose Hope, then she will be punished and the students will go free into a dead world. If even one student votes for Despair, they all stay in the school and Makoto gets punished. She almost succeeds in putting the students across the Despair Event Horizon...
... And then Makoto happens.
Makoto embraces his role as a Hope Bringer and manages to rouse the others out of their despair, causing Kyoko to christen him the 'Ultimate Hope'. All the students vote for Junko, much to her surprise... but once she gets over it, she's estastic. Having her plans fail at the last minute, imminent Cruel and Unusual Death... how can you despair more than that?
So Junko executes herself via every previous execution, glorying in her own despair all the while- except in the last half-second, when the crusher that was going to kill her pauses for a bit. The surviving students use the Escape Switch she had to leave school, with the hope that they can build new lives out in the world, and perhaps that Junko was lying about how bad things were.
The end!
