Watanuki Kimihiro can see spirits and other assorted supernatural creatures, which is quite a bothersome ability he strongly dislikes. On the way home one day, while plagued by some spirits, he is inexplicably compelled to enter a strange house. There, he encounters Yuuko, a mysterious woman who claims to be able to rid him of the ability to see and attract the troublesome creatures—for a price. She demands that he work at her "store" that grants wishes to people, and thus begins Watanuki's adventures through weird and wonderful events.
The series' protagonist is Kimihiro Watanuki, a high school student plagued by yōkai and ayakashi spirits. One day, when running away from the spirits, he accidentally enters the shop of witch Yūko Ichihara, who has the power to grant wishes for a price. Yūko decides to grant his wish of making his demons go away in exchange for having him work as her assistant in her shop. Working at Yūko's shop, Watanuki encounters various spirits and also gets to know his classmates Shizuka Dōmeki and Himawari Kunogi better. Although Watanuki comes to value his new life at the shop, he begins to worry about Yūko and eventually promises that he will try to grant her wish, should she have one.