Kimihiro Watanuki is a high school student plagued by ayakashi spirits, both of which are invisible to everyone else but him. The series begins when Watanuki stumbles, seemingly by chance, into a shop that grants wishes. The shop is owned by Yūko Ichihara, a mysterious 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 Yūko, must be of equal value; so, as payment, he must become Yūko's temporary, part-time cook and housekeeper.

Love is unusual for Koizumi Risa and Ootani Atsushi, who are both striving to find their ideal partner in high school—172 cm tall Koizumi is much taller than the average girl, and Ootani is much shorter than the average guy at 156 cm.

Once a year the prestigious Rikkyouin High School has a lottery to determine the next year's Student Council membership. On their first day of school Chihiro Enomoto wins the presidency while his childhood friend Tokino Akiyama picks the vice-president's ticket. There is one catch though, they must first pass a one year apprenticeship under the current Student Council and failure to perform the tasks assigned, however minor, will result in immediate expulsion from the school.

Invited to a wealthy client's mansion, time-traveling witch Yuko and her companions arrive to find a group of collectors assembled to participate in a mysterious auction. And the mystery only deepens when the collectors go missing one by one. As more guests disappear and strange occurrences abound, Yuko and her friends realize they must solve the mystery before they vanish as well.

It has been several years after the events of Shunmuki and Watanuki has become the new proprietor of Yūko's shop following her death. Domeki has taken a position at a university to study folklore and Kohane has become a student at the same university studying under Domeki. Due to Domeki's position, a series of events have occurred that requires Watanuki's services. The episode outlines the process by which Watanuki fulfills the request while presenting changes in many of the characters in the series. The ending theme is "Kaza Nagi" (風なぎ?) by Shikao Suga.