Following the events of Danganronpa 2: Goodbye Despair, Makoto Naegi, the Super High School Level Hope, is placed under arrest by the Future Foundation for harboring the Remnants of Despair; those who continued the evil desires of the Super High School Level Despair, Junko Enoshima, following her death. The top members of the Future Foundation, including Makoto's former classmates Kyoko Kirigiri, Aoi Asahina, and Yasuhiro Hagakure, are all brought together to discuss Makoto's punishment. Just then, the Future Foundation's headquarters is attacked by a missile, cutting off all exits, before a round of sleeping gas knocks everyone unconscious. When they wake up, the members are greeted by the all-too-familiar visage of Monokuma, who announces that a new killing game has begun before revealing that housekeeper Chisa Yukizome has already been killed.