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

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.

Natsume's secret is found out by Sasada, the class president, during the "Trial of Courage." She asks for his help to find the spirit that lives in the abandoned school. Natsume denies the fact that he can see anything, but she won't take no for an answer. Meanwhile, the spirit, Shigure, captures the rest of their school mates, in fury of the school being torn down...

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...

Natsume is possessed by a swallow spirit, who wishes to meet a human who once helped her. Natsume agrees to help her and the two grow attached. When Swallow finds the human, Natsume feels bad that she can't actually meet him, but when he hears of a kimono that can turn a spirit into a human for a day, he looks for it.

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.