Sakura Kusakabe, a mere junior high student, has committed a horrible crime. Or, rather, he will commit a crime—20 years into the future. The crime in question? He will prevent all women from developing past the age of 12, with immortality as an unintended side effect. As a result, the angel Dokuro Mitsukai is sent from the future as an assassin, armed with with a magical spiked bat named Excalibolg. However, rather than kill him, Dokuro wants to take a different approach. She resolves to be a constant nuisance to Sakura, in an attempt to prevent him from focusing on anything long enough to create his criminal technology. With Dokuro going against orders, the angel Sabato is sent out to complete Dokuro's mission. Between the impulsive Dokuro—who often murders Sakura with her bat before reviving him with the magic words Pipiru piru piru pipiru pi—and the electric baton-wielding Sabato, Sakura's life will never be peaceful again.

Ten years ago, a fairy by the name of Daisy appeared and asked the child Eiji Hoshimiya what his one and only wish was. Although his wish remains a mystery, the consequences were catastrophic. In an event called the Great Destruction, the world started to fall apart as everything collapsed and countless people died. Now, Eiji is a high school student whose only concern is his sick sister. He does not remember what he wished for; all that he remembers is that his wish caused the Great Destruction. In the years since that event, thousands of other people have also received abilities to make their heart's desire come true. These people called Orders are believed to be evil and are hated by the general public. However, some of these Orders are after Eiji's life in vengeance for those that he killed. Will Eiji be able to survive the numerous assassination attempts? And the biggest mystery of all: what did he wish for, and what were his intentions in wishing for something that caused so much desolation?

The Future Foundation is in shambles after the Final Killing Game and the revelation of the true culprit. As a desperate plot arises from one of the survivors to rid the world of despair once and for all, the remaining Future Foundation members must band together to stop this atrocity from taking place. Fortunately, they find themselves with help from a group of unlikely allies as they race against the clock to stop their world from being changed. In this finale to the Hope's Peak storyline of the Danganronpa series, the players in this neverending death game begin to understand the true meaning behind despair, hope, and atonement.

The name Tarou Sakamoto once instilled fear in every villain. No other professional hitman matched his prowess, and fellow assassins revered him. However, Sakamoto fell in love. In five short years, he married, became a father, put on some weight, and traded his weapons for an apron as he became the owner of a humble convenience store. Although Sakamoto is decidedly retired, he finds his old life of crime hard to shake off. His former partner, Shin Asakura, reappears and resolves to stay with Sakamoto's family under their strict no-kill rule. To make matters worse, a large bounty is placed on Sakamoto's head. Numerous assassins now pursue him—but they are in for a surprise. Sakamoto has not lost his edge, and no matter what tricks his enemies pull, he will fight off every last one to protect his dear family.