Single father Kakushi tries to hide his job as an adult manga creator from the daughter he adores, a scheme that gets more elaborate as she grows.

The story centers on Koyomi Araragi, a third year high school student who has recently survived a vampire attack, and finds himself mixed up with all kinds of apparitions: gods, ghosts, myths, and spirits.

Yato and Yukine have finally mended their relationship as god and Regalia. As a minor and unknown deity, Yato continues to take odd jobs for five yen apiece in hopes of one day having millions of worshippers and his own grand shrine. He has yet to fix Hiyori Iki's loose soul, but she cheerily prepares for high school nonetheless.

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.

Due to an unusual ability to see strange creatures called youkai, Takashi Natsume has never fit in. Over time, he has accepted that no one would ever believe him and has closed himself.

When Natsume accidentally breaks an intangible barrier, he frees Madara—a mighty spirit in the form of a lucky cat. Madara notices that Natsume bears a remarkable resemblance to his late grandmother Reiko Natsume, an outcast girl who created the Book of Friends. It is now in Natsume's possession.

With no interest in its powers, Natsume decides to keep the book for the sake of his grandmother's memories and to protect it from scheming youkai. Therefore, he makes a deal with Madara: he will hand him the book once his time is up, and in turn, Madara will act as Natsume's unofficial bodyguard. With his newfound goal of freeing those Reiko had sealed, Natsume's relationship with both youkai and humans slowly begins to improve.