The world consists of two parts: the near shore and far shore. The near shore is the place where people reside, while the far shore is the place for deities and ayakashi, which are emotional fragments that can posses humans and cause trouble. So it is a deity's responsibility to remove those ayakashi from the near shore with the help of weapons called Shinki, made from the spirits of dead people.

Yato is a minor deity of war without shrine. Together with his Shinki, Tomone, he runs a Delivery Wish Granting Service, granting wishes for only 5 yen. After his Shinki leaves him on less than agreeable terms, he decides to run simple errands that do not involve ayakashi-related matters. While on a mission to find a lost kitten, he is nearly hit by a bus, but saved by a girl named Iki Hiyori. Hiyori dies for a moment, but then comes back to life. This, however, causes Hiyori's soul to become unstable, leaving her body frequently. So by offering 5 yen, she asks Yato to fix her body... but Yato cannot help without a Shinki, so Hiyori accompanies him on his journey to find one, in the hopes of becoming normal again. But behind Yato's kind-hearted face lies a twisted past...