Death is one of many mysteries that has left humanity in the dark since the dawn of time. However, the burning question of what happens to the soul after one dies is soon answered to 17-year-old Yuzuru Otonashi. Waking up with no previous memories in a dimension between life and death, he discovers the unsettling truth of the afterlife. Taking the form of a high school, this bizarre dimension is designated to shelter those who died unwanted deaths. Feeling wronged by God during their earthly lives, the school's residents have decided to form the Afterlife Battlefront—a rebellious faction determined to oppose their god-like student council president, Kanade Angel Tachibana. The group's leader, Yuri Nakamura, recruits Otonashi in their fight against Angel in order to take control of their own lives. However, questioning the morality behind their actions, Otonashi takes a step behind the enemy lines to understand the opposing side of their common fate.

The year is 1274. After conquering most of the known world, the Mongols turn their sights on Japan and their first step on the road to a full invasion of the mainland is taking Tsushima Island. Kuchii Jinzaburou and a group exiles are sent by the Kamakura Shogunate to the island at the request of Princess Teruhi. There they will face overwhelming odds and the fate of Tsushima will be decided!

Jinta Yadomi is peacefully living as a recluse, spending his days away from school and playing video games at home instead. One hot summer day, his childhood friend, Meiko Menma Honma, appears and pesters him to grant a forgotten wish. He pays her no mind, which annoys her, but he doesn't really care. After all, Menma already died years ago. At first, Jinta thinks that he is merely hallucinating due to the summer heat, but he is later on convinced that what he sees truly is the ghost of Menma. Jinta and his group of childhood friends grew apart after her untimely death, but they are drawn together once more as they try to lay Menma's spirit to rest. Re-living their pain and guilt, will they be able to find the strength to help not only Menma move on—but themselves as well?

A year can change a person's life forever. The 365 days Class 3-E of Kunugigaoka Junior High spent with their eccentric teacher, Koro-sensei, certainly did. Carrying the memories of that year close to their hearts, alumni Nagisa Shiota and Karma Akabane return to their former classroom to recall the events of that momentous time of their lives. Nagisa and Karma are reminded by the familiar rooms, desks, chalkboard, and the class album of the events that shaped them into assassins and prepared them for the real world. That is the legacy of their octopus-like teacher—who had introduced himself by threatening to destroy the world if they didn't kill him by the end of the school year—and the time spent in the bizarre yet exceptional Assassination Classroom.