Michiru is a first-year student at a remote mountain boarding school with a notably large clock tower. On his first day, he accidentally breaks an expensive-looking statue. As punishment, both he and the boy involved are assigned to the school's Bureau for the Investigation of Special Affairs, headquartered in the underground library. A girl with an apathetic expression is already waiting there. She explains: magic exists in this school. When the clock tower chimes, a phenomenon called the Realm of Night merges with the school building, and magical disturbances follow. The Bureau handles them.