Hitsugi no Chaika is about the quest of a pretty and charming 14-year old sorceress named Chaika Trabant, who carries a coffin on her back. She is surprisingly adept in casting high-precision spells, but she has no memory of her past. The only thing she knows is to gather the scattered remains of Emperor Gaz. Toru Acura is a Saboteur who relies on his adoptive sister Akari for their food. After the fall of Gaz Empire, he finds it difficult to land a job until he meets Chaika in the woods, and agrees to help her accomplish her quest along with Akari.

The unlikely trio sets on the journey with a clear goal in mind, unaware of the dangerous truth.