After vanquishing another boss and stepping through the gates of the fifth floor, the misfit duo Kazuto "Kirito" Kirigaya and Asuna Yuuki are greeted with a beautiful landscape of crumbling ruins and catacombs steeped in mystery. This idyllic adventure is short-lived, however. Tensions between the Dragon’s Knights Brigade and the Aincrad Liberation Squad—the two leading guilds focused on clearing Sword Art Online—continue to rise and threaten the fragile stability of the frontline raiding group. Kirito and Asuna are forced to act quickly, making a desperate gamble and gathering a small number of allies for a dangerous mission. As a result, Asuna and Misumi "Mito" Tozawa must come to terms with their relationship after the near-tragedy that forced them apart on the first floor.

Empty classrooms, boring days. It was supposed to be a normal summer vacation just like any other. Suddenly, the school begins to drift through another dimension, and 36 boys and girls are left there, awakening to their supernatural abilities. Amidst the whirlpool of questions that come to mind one after another, survival in a supernatural world begins.

The chaotic aftermath of a confrontation between Jinka Yamato and Yazen results in the power dynamics between the magically gifted katawara and humans being turned upside down. As the news of the downfall of dangaishu—the katawara-hunting monks led by Yazen—spreads across the country, rogue groups of katawara start to form, worsening the already-fragile relationship between them and humanity. Having lost faith in his abilities, Shinsuke Hyoudou now spends his time heavily drinking in the company of Senya, a former enemy of his who controls one thousand katawara within his body. Senya indirectly causes the death of the father of Tsukiko, his newfound friend, after a surprise attack of a local god gone berserk. Despite the circumstances, Tsukiko holds no grudge against Senya and is determined to become Shinsuke's disciple no matter what. Although Shinsuke refuses to become Tsukiko's sword instructor, he reluctantly agrees to let her travel with him and Senya. While the unlikely trio heads towards their next destination, Tama Youko continues her journey to find the trail of Jinka, the nine-tailed fox who has the power to destroy the world.

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. [Written by MAL Rewrite]