The main character, Natsume Tomoharu, takes the opportunity to live on his own when he enters high school. Although he appears to be a normal high school student at first glance, there is one thing about him which isn't normal. He's haunted by the ghost of a young girl, Minakami Misao.

Tomoharu moves to his new place of residence, Meioutei, and starts enjoying a carefree high school life. But this is all ruined when a beautiful girl named Kurosaki Shuri appears with a trunk which Tomoharu's brother told her to pass on to Tomoharu. The presence of the trunk causes the appearance of Takatsuki Kanade, a girl dressed like a shrine maiden who is after the trunk.

Because Tomoharu is in possession of the trunk, he will come face to face with the the hidden truth of this world.