Watanuki Kimihiro is a high school student plagued by youkai and ayakashi, spirits with a strong attraction to him. The spirits are invisible to others and encounters with them are extremely troublesome. When he stumbles into a shop that grants wishes, however, events in his life promise to become more unusual.
The shop is owned by Ichihara Yuuko, a mysterious and beautiful (sometimes playful) witch of many names and esoteric renown. For a price, she offers to grant Watanuki's wish to be rid of the spirits. The price, according to Yuuko, must be of equal value and so, as payment, he temporarily becomes Yuuko's part-time employee.
Watanuki's job consists of small errands dealing with the supernatural and household chores. His love interest, Kunogi Himawari, and "rival", Doumeki Shizuka, occasionally join him in his work as per Yuuko's request. The three become increasingly close despite Watanuki's annoyance with Doumeki.