The story is set in a fictional world where fifteen years earlier, people stopped giving birth, and even with their bodies damaged beyond repair, the dead can not find rest, unless they are buried by mysterious individuals known as "gravekeepers". According to legends, this happened because by that time, God had abandoned the world. Ai Astin, a young gravekeeper, has her life changed forever when an immortal gunslinger named Hampnie Hambart shoots everyone in her village except for her. Having no place left to live, Ai ends up relying on the same man who killed everyone around her as she travels the world to perform her duties as a gravekeeper and to learn more about the reasons why the world had reached such a state.
As she goes along her journey, she meets new people: Hampnie's childhood friend Julie, the gravekeeper Scar, a mysterious boy named Alice and a ghost witch who goes by Dee. When Hampnie leaves her due to circumstances, Ai and her new companions travel the world, with the goal of fulfilling her dream of saving the world.