At the boundary between this realm and another, there live eight million gods, dead spirits who serve the gods, and other assorted spirits who help and meddle in the affairs of humans. A sweet middle school girl named Hiyori Iki has been enduring bullying from her classmates, and she goes to the restroom by herself to cry. Scrawled on the bathroom wall is a phone number and the message, “I solve your troubles.” After Hiyori calls the number, she encounters a homeless boy wearing a jersey who calls himself a god. The boy, named Yato, is rough, moody, lazy, and never listens to anyone’s wishes, but he had the power to be a god… that no one knew of

In times of need, if you look in the right place, you just may see a strange telephone number scrawled in red. If you call this number, you will hear a young man introduce himself as the Yato God. Yato is a minor deity and a self-proclaimed "Delivery God," who dreams of having millions of worshippers. Without a single shrine dedicated to his name, however, his goals are far from being realized. He spends his days doing odd jobs for five yen apiece, until his weapon partner becomes fed up with her useless master and deserts him. Just as things seem to be looking grim for the god, his fortune changes when a middle school girl, Hiyori Iki, supposedly saves Yato from a car accident, taking the hit for him. Remarkably, she survives, but the event has caused her soul to become loose and hence able to leave her body. Hiyori demands that Yato return her to normal, but upon learning that he needs a new partner to do so, reluctantly agrees to help him find one. And with Hiyori's help, Yato's luck may finally be turning around.

In the second season of Noragami the main focus is on Bishamon, god of combat. She has many shinki due to her being unable to abandon spirits attacked by Ayakashi. She has a large group of shinki with her as leader, causing her trouble as she sometimes cannot tend to all of them properly, especially when one of them gets sick or is in pain. She has a strong hate for Yato, as a dark past binds the two of them. How will the horrifying events dated hundreds of years ago in combination with current evil happenings affect Yato and Yukine?

Yato and Yukine have finally mended their relationship as god and Regalia, and everyone has returned to their daily life. Yato remains a minor and unknown deity who continues taking odd jobs for five yen apiece in the hopes of one day having millions of worshippers and his own grand shrine. Hiyori Iki has yet to have her loose soul fixed by Yato, but she enjoys life and prepares to attend high school nonetheless. Taking place immediately after the first season, Noragami Aragoto delves into the complicated past between Yato and the god of war Bishamon. The female god holds a mysterious grudge against Yato, which often results in violent clashes between them. It doesn't help that Bishamon's most trusted and beloved Regalia, Kazuma, appears to be indebted to Yato. When lives are on the line, unraveling these mysteries and others may be the only way to correct past mistakes.