When Mishiro was small, half of his soul was eaten by a toothed deity. Since then he has had to deal with spirits called kotowari that reside in the darkness of the souls of people who are related to him, no matter how distant.
Kotowari are soul fragments created from a person’s suffering and they can normally only be seen, heard and touched by that individual. Even if the kotowari is destroyed, it will keep respawning unless the cause of the suffering is resolved. Shortly after transferring to a school in a history-laden sightseeing town, Mishiro encounters a kotowari and decides to search for its owner.
However, there isn’t just one kotowari as many other girls harbour their own suffering.