Natsume discovers that the heirloom "Book of Friends" that his grandmother, Reiko, gave him possesses the names of the spirits she defeated and bound to her will. Assisted by a cat whom Natsume addresses as Nyanko-Sensei (lit. Master Little Meow), Natsume aims to return all of the names to their rightful owners.

Natsume is implored to help spirits who are currently being exorcised. He finds a kindred spirit in Tanuma, a boy who also senses spirits although not as powerful as Natsume.