Yato is a minor deity who lacks even a single shrine. In order to build his own shrine, he will need some help. Hiyori, the daughter of a respectable family, is almost in a traffic accident, but is rescued by Yato. This causes her to chase Yato down, and they begin to work together. Yato also finds a boy named Yukine who becomes a "sacred treasure" that can be used by a god. The three of them battle "you" who brings harm to humans as Yato's hidden history is gradually revealed.