Yato is a minor deity who lacks even a single shrine. In order to build his own shrine and gain recognition as a god, he scrawls his cell number on the wall of a downtown bathroom telling people he will help them in exchange for a 5-yen offering, becoming a self-styled "delivery god." Hiyori, the daughter of a respectable family, is almost killed in a traffic accident, but is rescued by Yato. This causes her to become a "hanyou," a person who can exit her body in soul form.

She chases Yato down, and they begin to work together to help Yato be recognized. Yato also finds a boy named Yukine who becomes a Regalia, a "sacred treasure" that can be used by a god as a weapon to fight. The three of them battle phantoms who bring harm to humans as Yato's dark hidden history is gradually revealed.