Chihiro Fujisaki, a Teen Genius and expert computer whiz, is invited to attend Hope's Peak Academy, a prestigious school for students with exceptional talents, as the Ultimate Programmer. Upon entering, he loses consciousness and wakes up in a locked-down school alongside 14 other students. They are greeted by Monokuma, a sadistic robotic bear, who informs them that they are trapped in a killing game: to escape, they must murder a classmate and get away with it during a Class Trial. If the killer is caught, they are executed; if they succeed, everyone else dies. With no way out, tensions begin to rise.
After discovering that their captor is monitoring them, the students attempt to adapt to their new reality. Unfortunately, it doesn't take long for someone to crack, and one morning, Leon Kuwata, the Ultimate Baseball Star, is found dead. The students enter their first Class Trial where they try to figure out who killed Leon so they don't all get executed. Evidence reveals Sayaka Maizono, the Ultimate Pop Sensation, killed Leon and tried to frame Makoto Naegi, the Ultimate Lucky Student, when Monokuma threatened her with the lives of her closest friends. She is voted guilty and is executed by Monokuma in a stage show themed execution.
Monokuma provides new motives: each student receives a personal letter containing a dark secret about themselves. When faced with his own secret, Chihiro meets Mondo Owada, the Ultimate Biker Gang Leader, intending to get strong enough so that he can tell people the truth on his own. Mondo Owada, afraid his own secret (killing his brother in an accident) would come out, attempts to kill Chihiro in a fit of jealous rage, but unlike in canon, slips up. Chihiro forgives and comforts him, but despite the close call, they still go back to the changing room early in the morning to find Toko Fukawa, the Ultimate Writing Prodigy, lying dead face down in the swimming pool. Chihiro reveals during the trial that he is biologically male but disguised himself as female to escape his past as a weakling, all so he doesn't get framed for the crime. It's also revealed that Toko had a split personality, one half of which was the serial killer, Genocide Jack, who everyone believed was the Mastermind behind their predicament. Toko's killer is revealed to be Aoi Asahina, the Ultimate Swimming Pro, who fought and killed Toko in self-defence. She is executed in an execution themed around a water tank trick, where she is eaten by sharks.
Chihiro begins to employ the use of Alter Ego, an AI copy of himself, to find more information on the Killing Game, while Monokuma introduces a cash reward for murder. At first, it doesn't work, so later, Monokuma introduces an additional prompt: That if someone kills two students, and gets away with the crime, they will be able to leave the academy and no one else gets executed. Shortly after, carnage ensues, with Sakura Ogami, the Ultimate Martial Artist, and Hifumi Yamada, the Ultimate Fanfic Writer, both found dead, as well as Kiyotaka Ishimaru, the Ultimate Moral Compass, knocked out and critically injured. The trial reveals that Celestia Ludenberg, the Ultimate Gambler orchestrated the whole thing, manipulating Hifumi into killing Sakura before she planned to kill Hifumi and Taka herself. However, her plan failed because Yasuhiro Hagakure, the Ultimate Clairvoyant, walked in on Hifumi killing Sakura, nullifying the additional motive. In his attempt to silence Hiro and reclaim the bonus, Hiro lures Hifumi into the trash room, and turns the tables on him. Hiro is executed in a game-show style execution where he is eaten by a carnivorous door.
Tensions are inexplicably high following Hiro's execution, especially since Celeste managed to get away with her own crime scot free on account of not actually killing anyone. On top of that, Byakuya Togami, the Ultimate Affluent Progeny, and Kyoko Kirigiri, the mysterious girl who hasn't revealed her talent, are remaining distant for their own reasons, while Makoto declares that he will no longer associate with or trust the group. When things seem like they can't get any worse, Junko Enoshima, the Ultimate Fashionista, is revealed to be Mukuro Ikusaba, the Ultimate Soldier, in disguise, and a mole for Monokuma, blackmailed to betray the others. Makoto makes peace with Kyoko and Chihiro after some soul-searching, and after Kyoko reveals to them both that her memories were erased, which is why she does not know her own talent. Unfortunately, after Alter Ego is executed by Monokuma, Celeste ends up dead, crushed by a piano in the music room. The others initially suspect one another, but the ultimate truth is even more shocking - The killer is none other than Makoto, who took Celeste out to either defeat or lure out the true mastermind. This revelation devastates everyone, including Byakuya, and especially Mukuro, who secretly had feelings for him. Makoto is executed with a sword-in-the-barrel execution, but his final words rouse everyone to work together to fight back against Monokuma.
Now the Mastermind of the Killing Game is getting desperate. The class is united against them. Nobody is biting at any of their motives. But soon after, Chihiro, Kyoko, and Byakuya are locked in a freezing cold bio-lab, and the lights are shut off. When the lights come back on, Byakuya is lying dead at Kyoko and Chihiro's feet, apparently killed by one of them, or so the setup suggests. When Chihiro fails to provide sufficient proof, he is sentenced to execution. At the last moment, Alter Ego, who was actually alive the whole time, intervenes, allowing Chihiro to survive, but he is thrown into solitary confinement.
Kyoko and Mondo free Chihiro, and together they uncover the school's secrets. They learn that Hope’s Peak Academy had been barricaded for years, and the students had lived there before their memories were erased. Mukuro was not just another student—she was Monokuma’s enforcer and the sister of the true mastermind, the real Junko Enoshima. Junko, the Ultimate Despair, reveals herself and confesses to framing Chihiro and Kyoko for Byakuya's murder, being the real perpetrator in an attempt to rid herself of Kyoko's investigative ability as the Ultimate Detective. She also confesses to orchestrating The Tragedy, a world-ending event that plunged society into chaos. The killing game was her form of entertainment, reveling in despair. She gives the survivors a choice: stay trapped in safety or escape into the ruined world. Even though Junko almost defeats them, the voices of those that were lost rouse Chihiro back to his senses, and he does the same in kind for his surviving group. The students reject despair, voting for hope instead, and Junko, relishing her own despair, executes herself in a compilation of previous executions. With Monokuma deactivated and the doors unlocked, Chihiro, Alter Ego, and the remaining survivors—Kyoko, Mondo, Taka, and Mukuro—step into the outside world, uncertain of what awaits them.