In modern day Japan, humans with "divine power" are called "Himiko," and once receiving national certification, they are called "Kamisama" or "God." After Nagi's grandmother passes away, the shrine in her hometown no longer has a god and is in trouble. Nagi's twin brother, Takeru, inherited divine power but unfortunately is a hikikomori or shut-in.

By chance, Nagi enrols in "Kamisama Gakkou," the school where Himiko attend. Compelled to revive the shrine, Nagi aims to receive national qualification and become a god.