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 visited by the village's local god who is currently fading because of the lack of devotees.

Natsume comes across an old ticket in Reiko's belongings and decides to go to the abandoned train station to see why she kept it. There, he meets a slow witted spirit named Santo, who was waiting for Reiko the entire time to go Kiriganuma, to see and make up with his friend, Mikuri, but the trip isn't as easy as it first seems...

When Natsume finally has enough of Nyanko's behavior, Nyanko leaves, wandering about by himself and causing trouble.

Tanuma finds out that Nyanko-Sensei is a spirit. Tanuma and Natsume enjoy the autumn festival and previous acquaintances are seen again.

Natsume meets a shrine god in the form of an elderly woman. He is forced to help her return a mirror to a youkai said to bring disaster. The youkai turns out to be Reiko, Natsume's grandmother, who the shrine god only mistook as a youkai. Reiko had lent out the mirror so that the shrine god could save the life of an old tree, but the two parted after Reiko learned that the elderly woman was a youkai.