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.

When 2% of the world's population abruptly disappears without explanation, the world struggles to understand just what they're supposed to do about it. This is the story of the people who didn't make the cut.