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Living alone after his parents passed away, Kimihiro Watanuki is a high school student who can see otherworldly creatures that are attracted to him. His days are plagued by these nuisances, and he wishes to rid himself of this inconvenience. One fateful day, as Kimihiro is being chased by a horde of spirits, his feet bring him into a mysterious store to seek shelter. Here he meets Yuuko Ichihara, the mistress of this supposed store, who claims to be able to grant wishes. Yuuko offers to grant Kimihiro's, as long as he pays an appropriate price.

Thus begins Kimihiro's time working in her store to earn the payment necessary for his wish. In Yuuko's employ, he must become further involved with spirits and the supernatural before he can leave that world behind. How will he fare in the inexplicable encounters that await him?