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

Natsume is dragged off into the cave of the evil spirit that is after Taki. He temporarily loses the ability to see youkai after being poisoned by the spirit. Will he be able to stop the youkai from eating Taki without his sight?

(Source: Wikipedia)

Natsume encounters a young boy named Kai sealed in a coffin in an abandoned house. Natsume sets Kai free and finds out that Kai is being stalked by a youkai. After a time, Natsume becomes the target of this youkai and stops the youkai's stalking with Nyanko-sensei's help. In the end Natori who turns out to be the stalker and who sealed Kai in the coffin, tells Natsume that Kai is a Youkai.

(Source: Wikipedia)

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.

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 encounters some strange, monkey-mask wearing demons while out in a forest. They want the book of friends, and start physically threatening him until Natsume is saved by Nyanko-Sensei. Later on, Natsume encounters the demons again and is captured by them, and brought to their forest. Meanwhile, Nyanko-sensei learns some interesting things about the forest the monkey mask demons live in. Running away from the demons, Natsume and Nyanko-sensei are unintentionally saved by an exorcist - Matoba! Not wanting to confront him, Natsume runs again but gets lost in the woods, and stumbles upon a house... belonging to the Matoba. Both he and Nyanko-sensei are captured, but manages to escape and find each other, though being lost in the house. The episode ends with Matoba finding Natsume saying, "It's been a long time, Natsume Takashi-kun.

Natsume is saved by Tanuma and the two escape from the banquet hall with the help of Natori, who was disguised as a youkai. Tanuma is drawn more into the world of the youkai and experiences it first-hand, which greatly worries Natsume. Blood marks are found all around the mansion and Natsume's fears come true when Tanuma is attacked by Omibashira, but is protected by a stone Natori gave him. After Natsume helps Natori seal Omibashira everyone is able to escape the previously sealed exits. Promising Tanuma that he'd tell him his complaints at school the next day, Natsume finally arrives back home.

Natsume, accompanied by Nyanko-sensei, set out to visit his old home. He visits a relative to pick up the key to the house, but is being followed by a youkai who wants him to draw a mouth for it. He leads the youkai away from the home of his relatives and Nyanko-sensei drives it away. When the two get back on track to finding the house, Natsume is suddenly attacked by the youkai and becomes lost in old memories.

On a rainy day, Natsume meets a young girl youkai. Her name isn't in the Book of Friends, but she wants his help anyway: she wants him to find a man she met once. The man couldn't see youkai normally, but a mischievous trick of the weather let him see her for just one day. For the next fifty years she visited him, hoping he'd see her one more time, but he never did. Now he's vanished. Can Natsume find him for her?

Natsume sees strange writing on the chalk board in the Earth Science classroom. Taki tells Natsume of the hairy yokai she helped leave her home. Natsume comes to Taki's home and learns that three yokai had been trapped there -- two "rabbit" yokai and a hairy white one. The hairy yokai is enchanted by Taki and helps find the rabbit yokai in Taki's home. Natsume learns the hairy yokai was the one who wrote on the school chalkboard and goes back to read the yokai's feelings on it.

A yokai known as "The Days Eater," turns Natsume back to a young child. Nyanko-sensei enlists the aid of Tanuma and Taki.

Natsume talks to a teenage boy at the station, who turns out to be a youkai that left a human because of their feelings for one another. The boy wants to find her because he received a wedding invitation.

Natsume decides to tell Natori about his secret, when the search for the seal room is over...