Kimihiro Watanuki is a high school student plagued by yōkai, supernatural beings magically attracted to him. The creatures are invisible to others, and as a result he feels extremely burdened by them. When he quite literally stumbles into a shop that grants wishes, his life changes drastically.

The shop is owned by Yūko Ichihara, a mysterious, beautiful witch of many names and esoteric renown. The seemingly all-knowing witch offers to grant Watanuki's wish to be rid of his ability to see spirits. However, in exchange, he must pay a price equal to the power required to grant the wish. Yūko discovers that Watanuki is very skilled with his hands and a hard worker. As a result, Watanuki is forced to perform housework and odd jobs for Yūko until he has done enough work for his wish to be granted.

Shortly afterwards, other characters become involved with Watanuki's position, including his love interest, Himawari Kunogi, and his "rival," Shizuka Dōmeki. The three become increasingly "friendly," despite the number of times Watanuki becomes annoyed by Dōmeki's calm demeanor.