15 years ago, the stories say, God abandoned the World. No new people are born, and no one can die. Gravekeepers charged with bringing peace to those aged or broken of body who cannot die naturally. This is what Ai has always believed to be her destiny, until a man she believes to be her father arrives in town and shatters her world-view.
In a world where natural death does not occur, Ai has become the new "gravekeeper" in her small village.
Ai meets Scar, a real gravekeeper, and Julie, a man hell bent on avenging his wife's death at the hands of Hampnie.
While on their journey to find Hana, Hampnie and Ai get ambushed. Hampnie gets caught, and Ai comes to a stunning realization.
Leaving Hampnie behind, Ai, Julie, Scar and a mysterious stranger head to Ortus, the city of the deceased.
Ai learns more about how Ortus came to be. Kiriko introduces her to the Princess, who befriends her immediately.
Ai has learned a terrible truth about her new friend Ulla: she is Koroshiohake. Ai wonders whether or not Ulla knows what she is really doing, and seeks her out to tell her the truth.
Ai is kidnapped and taken to Goran Academy, where she meets kids with special powers.
The plan to escape Goran Academy is set, but one student has doubts about reentering the outside world.
Ai sets off in search of Scar, using Celica as a compass needle to find her. The group then stumbles upon Story Circle, the place where grave keepers are born.
Alis, Ai and the group step into the world of Class 3-4, a pocket universe wished into existence by the wishes of a group of students.
Ai turns 13 in the world of Class 3-4, and Dee reveals the truth behind the reason why the world was created and why it endlessly loops.
Dee sees a world that she can never be a part of and resolves to forcefully reset the world. Alis and Ai try to stop her and a grand secret is revealed.