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

One day, Natsume finds a yokai named Kagejawan running around near his home, which he soon learns means disaster is about to strike.