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.

After fainting at work, a young lady awakens in the back room of the café she works at with no memory of her life or those around her. Two of her friends, whom she soon learns are named Shin and Toma, are called to help her get home safely. Once she is alone, she meets a spectral boy named Orion that only she can see and hear. He explains that she lost her memories because of his chance visit to her world, so he vows to help her remember who she is. However, regaining her departed memories without worrying those around her may be more difficult than she realizes. In addition to the gloomy Shin and the protective Toma, she must be wary of arousing the suspicions of the captivating Ikki, the quick-witted Kent, and a mysterious man who lurks in the distance. As her amnesia entangles her in the lives of each of these men, her fragmented memories return piece by piece, and the mysteries of her circumstances slowly come to light.

A trio of diabolical dragons stirs from eons of slumber deep within the earth. Charging to the surface, they launch a bloody rampage against humanity, feasting on the weak and gaining strength from their hapless victims' souls. It will take the power of ancient god Takegami, the Guardian of Darkness, to vanquish the evil serpent forces. But alas, the mortal body Takegami inhabits belongs to a host reluctant to fight.