Natsume meets the very first Yokai whose name was written in the Book of Friends.

Natsume takes in a strange origami doll that shows wonderful dreams.

Chobi is depressed because his favorite comb broke. Meanwhile, Natsume sees a white dragon in the sky...

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

Natsume goes to a dam and finds a town that had been submerged in water. Just then, Natsume gets possessed by a yokai and falls unconscious.

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

While outside during school Natsume is hit with a ball while reading. He goes to retrieve the ball and ends up breaking a Youkai's seal (much like he had with Nyanko-sensei). Later that night Natsume and Nyanko-sensei discover a look-a-like of Nyanko, only to have him steal the Book Of Friends!

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.

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 is accosted by a spirit who asks for her brother's name back. She says that both of them have come from the village of floating spring, a paradise sealed off from the land of men. Meanwhile, the local Youkai are happy that the local priest is no longer in his temple. Natsume worries for his friend Tanuma, the priest's son, but isn't sure what to say...

There is something killing Youkai and draining them of their blood. Natsume can't help but investigate and runs into old friends.

Natsume finds out who's been stealing the youkai blood: the exorcist Matoba Seiji. He investigates with the help of Natori, but is captured by Matoba's servant youkai. Matoba is willing to sacrifice any number of youkai for his own ambitions. He tells Natsume why he's gathering blood: to release the seal on a powerful youkai. Natsume learns that there are people who treat Youkai in a totally different way than he or even Natori.

Natsume is invited to go to a pottery classroom with Shigeru. It's being held in an inn where he once stayed. When he goes there, he meets an old friend: the young fox child he once saved.

Tanuma is experiencing how Natsume lives every day. While Natsume and the youkai gain an understanding.

A youkai from Natsume past has found him and memories of living with relatives before the Fujiwaras are explored.

After a brief incident in the forest, Tanuma has become distant to Natsume like he is avoiding something. In the meantime, there is something breaking glass around the school.

Natsume is approached by someone he knew from elementary school. He wants nothing to do with them, but they threaten to reveal his secret: that he can see Youkai, if he doesn't come along with them. He reluctantly goes with them, and is taken to meet a strange girl...

Midterms are over, and Natsume leaves on a trip with Nishimura, Kitamoto, and Sasada. He realizes that the scenery he's viewing from the train is from one of the places he grew up in, when he was passed around from one family to the next. He'd thought he didn't have any good memories of the time, but then he remembers what happened when he lived there...

Natsume helps clean the stoeroom at Taki's house with Tanuma. He realizes that one of the kimonos that her grandfather, who researched youkai, used to ward off demons was missing, but decides not to tell them so they won't be scared. But that kimono was an old doll youkai, who was trying to recover its body which was torn apart when her grandfather sealed it

Without Sensei to protect him, Natsume has to remain constantly on guard. But the pressure of keeping secrets from his friends is causing Natsume to break.

Touko and Shigeru are the kind elderly couple who took in Natsume when no one else would. But what were they like before they let Natsume move in?

Natsume meets a spirit who used to be friends with a man who could also see spirits, but one day lost this ability.

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

Natsume helps a youkai out of a pot, and as a "reward", is made young again. But Natsume is already young, and making him younger just confuses him and addles his memories. When he doesn't know who to trust, will he have the strength to know who his real friends are?