In the backwater town of Bellforest lives a 14-year-old boy named Renton Thurston. He desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure to brighten up his mundane life. However, stuck between his grandfather's insistence to become a mechanic like him and the pressure of his deceased father's legacy, the only excitement Renton finds is in his pastime of riding the Trapar wave particles that are dispersed throughout the air, an activity akin to surfing. Everything changes when an unknown object crashes through Renton's garage, discovered to be a Light Finding Operation—a robot capable of riding the Trapar waves—specifically known as the Nirvash typeZERO. Its pilot is a young girl named Eureka, a member of the Gekkostate, who requests a tune-up for the Nirvash. Their meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside Eureka as the co-pilot of the Nirvash.

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.

Knowing that he is risking his life, Kei Kurono makes the uncharacteristic decision to jump onto train tracks to save a homeless man from death, only to perish in the process. But when he comes to, Kei finds himself in a room with several other recently deceased people, as well as a large, mysterious black ball. While the people in the room are trying to make sense of their situation, the ball suddenly opens, revealing a cache of weapons and strange black suits. The ball then instructs everyone that they have to hunt down an alien and teleports them to an unknown location. With very little information to work off of, Kei teams up with his childhood friend Masaru Katou and an unfamiliar woman, and the trio explore their new surroundings. It quickly becomes apparent, however, that they have stumbled into a dark and dangerous world where anything could happen to them.

Upon witnessing a man's head cracked open with an axe, 16-year-old Yuri Honjou trembles in fear and confusion as she flees from the masked assailant, only to find out she's trapped in an abandoned building where every door is mysteriously locked. Desperately searching for a way out, Yuri runs to the rooftop, but a world with no signs of life stands before her, surrounded by high-rise buildings. Though filled with despair, once she learns that her brother is also in this strange place, Yuri is determined to find him and escape. However, she soon finds that there are more masked murderers in the area, anxious to terrorize their newfound victims and satiate their sickest desires, leaving Yuri to question if they will be able to make it out alive.