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.
かつて世界を崩壊させた『人類史上最大最悪の絶望的事件』―――超高校級の絶望と呼ばれた彼らは、世界各地で同時多発テロを敢行・・・それに対抗すべく組織された『未来機関』。招集された幹部の前に反逆者として引き出されたのは、かつての英雄・苗木誠だった。そして、そこに突然響くモノクマの声、「うぷぷぷ。今回は未来機関の皆さんに、コロシアイをしてもらいまーす！」
Después de los eventos de Danganronpa 2: Goodbye Despair, Makoto Naegi, la Super High School Level Hope, es arrestada por Future Foundation por albergar a los Restos de la Desesperación; aquellos que continuaron los deseos malvados de la desesperación de nivel de la escuela secundaria superior, Junko Enoshima, después de su muerte.
Makoto Naegi, viene arrestato dalla Fondazione del Futuro, accusato di aver salvato i rimanenti della Disperazione: coloro che hanno continuato i desideri di Junko Enoshima dopo la sua morte.
Makoto Naegi perde a eleição enquanto a batalha entre a Fundação do Futuro e os Remanescentes do Desespero continua!
Après les événements de Danganronpa 2 : Goodbye Despair, Makoto Naegi, l'Ultime Espoir, est arrêté par la Fondation Future pour avoir hébergé les Vestiges du Désespoir, ceux qui ont poursuivi les désirs maléfiques de l'Ultime Désespoir, Junko Enoshima, après sa mort.
