It looked like it would be a normal day for Ganta Igarashi and his classmates—they were preparing to go on a class field trip to a certain prison amusement park called Deadman Wonderland, where the convicts perform dangerous acts for the onlookers' amusement. However, Ganta's life is quickly turned upside down when his whole class gets massacred by a mysterious man in red. Framed for the incident and sentenced to death, Ganta is sent to the very jail he was supposed to visit. But Ganta's nightmare is only just beginning. The young protagonist is thrown into a world of sadistic inmates and enigmatic powers, to live in constant fear of the lethal collar placed around his neck that is slowed only by winning in the prison's deathly games. Ganta must bet his life to survive in a ruthless place where it isn't always easy to tell friend from foe, all while trying to find the mysterious "Red Man" and clear his name, in Deadman Wonderland.

After Makoto Naegi and his fellow survivors escaped Hope's Peak Academy to the world beyond, they soon join the Future Foundation, an organization dedicated to combating despair. Just when all seems to be looking up, Naegi is arrested and tried for betrayal due to defending a malicious group of Remnants of Despair. Standing before all of the Future Foundation executives, he finds himself, along with Kyouko Kirigiri and Aoi Asahina, facing an unknown fate. The matter at hand only escalates when the organization's supposedly impenetrable security is hacked into by a familiar face: Monokuma. Much to Naegi's horror, the mechanical bear immediately announces the beginning of a new killing game, as moments later, the first victim appears as a signal for despair to resume its brutal conquest. Naegi, the Super High School-Level Lucky Student, must once again unravel the mystery as his colleagues and friends begin falling around him. However, there are no more class trials; among the 16 desperate participants, there is only one killer—and their death means the end of this infernal game.

A bus full of eccentric individuals is headed towards the urban legend known as Nanaki Village, a place where one can supposedly start over and live a perfect life. While many have different ideas of why the village cannot be found on any map, or why even the police cannot pinpoint its location, they each look forward to their new lives and just what awaits them once they reach their destination. After a few mishaps, they successfully arrive at Nanaki Village only to find it completely abandoned. Judging from the state of disrepair, it has been vacant for at least a year. However, secrets are soon revealed as some of the group begin to go missing while exploring the village and amidst the confusion, they find bloody claw marks in a forest. As mistrust and in-fighting break out, will they ever be able to figure out the truth behind this lost village?

Hope's Peak Academy's unconventional class 77-B is about to have an even more eccentric addition: Chisa Yukizome, an alumna with the title of Super High School-Level Housekeeper—and their new homeroom teacher. Cheerful, passionate, and capable, Chisa immediately sets about correcting the students' problematic behavior and strengthening their relationships. It may not be easy dealing with diverse pupils ranging from princesses and nurses to yakuza and impossibly lucky students, but anything is possible with the power of hope. Meanwhile, Hajime Hinata, an unremarkable boy from the school's Reserve Course, longs for a talent. One day, he has an unexpected meeting with class 77-B's Super High School-Level Gamer Chiaki Nanami, who presents to him a new, hope-filled outlook on life. However, unbeknownst to him, the school's upper echelon is about to execute a sinister project centered around Hajime that will bring Hope's Peak—and the rest of the world—to its knees. Zetsubou-hen chronicles the daily lives carried out at the talent-cultivating academy, and the darkness that lurks beneath. As despair slowly infects hope, plans are put into motion to start the Biggest, Most Awful, Most Tragic Event in Human History, and the end begins.