Mikuriya Jin decided to use a piece of the sacred tree to carve a statue for his middle-school project and while moving it outside, the statue happens to touch the ground transforming into a cute girl. Her name is Nagi, a Shinto spirit, the guardian of the village, and she is really annoyed that her sacred tree was cut down.

Having no place to live, Nagi is forced to move in with Jin and tries to accept her new existence by venting her anger against bugs by squashing them... by cleaning the "impurities".

Nagi has a rival in a little sister guardian deity, who lives in a shrine located on the other side of the river. Well, Zange-chan has woken up too and decides to become the top teen-idol of the village, much to Nagi's dismay.