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!

While fooling around in the snow, Natsume and Nyanko-sensei run in to Gen, a forest guardian who lives inside a statue. Gen tries to take over Natsume's body, but instead takes over a snow rabbit that Natsume had made. Gen pleads Natsume to help him find an evil spirit who destroyed Sui, his guardian partner, and Natsume agrees. But it seems Gen isn't telling everything he should...

Natori invites Natsume on a Hot Spring trip. But noises from the closet and a kimono-clad figure dangled from the ceiling make Natsume uneasy. Not wanting to trouble Natori because of his kind gesture to enjoy the Hot Spring with him, Natsume investigates the Hot Spring himself. During the night Natsume meets with the Youkai, where she comments that he is too soft, and attacks!

Natsume takes care of an abandoned egg from a nest, not considering it could be a Youkai. After it hatches, it turns out it is a rare baby spirit called Tatsumi, who thinks that Natsume is its parent. Natsume can't help but get attached to the little spirit even as Tatsumi grows tired and sick. But as Natsume takes care of Tatsumi, a mysterious spirit comes and wants to take away Tatsumi for his master... who wants to eat him!

Natsume encounters a spirit who was enslaved by his grandmother Reiko 50 years ago by writing his name on a torn page from the Book of Friends, and tying it to a tree in a forest. Can Natsume help locate the torn page? What was Reiko's intention of tying it to a tree?

There is a new girl in school, Taki Tooru. With her appearance at the school, circles resembling crop circles begin to appear. As Natsume tries to find out more about the circles and Taki, he is visited by another Youkai. Only this time the Youkai isn't looking for his name, but for a snack.

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?

Natsume, Kitamoto and Nishimura take a trip to an old inn to spend some quality time doing their homework. Surrounding the inn is a lake; that is believed to be home to a mermaid.

From the day that a picture of a row of cherry trees in a desolate winter was obtained, every time Natsume wakes up, his rooms is covered in petals. Trying to solve the root of this activity, Natsume and Nyako Sensei try and return the picture to Miya, a shadowy figure who accompanies the picture. But why can't they return it to Miya...?

Mysterious footprints and markings are left on the gate of the Fujiwara house. Strange things start going on inside the house and Shigeru verifies with Natsume that the cause of this activity involves the husband and wife who used to live there. And so Shigeru tells story of those two but in a unusually childlike manner...

After chasing an injured yokai around, Natsume encounters Natori, who then invites him to go to a meeting of sorcerers. There, Natsume meets others with similar powers and similar problems.

At a house rumored to be haunted by ghosts, Natsume hears the voice of a child. Following the voice to its source, Natsume finds a child named Kai, who is trapped in a casket-like box. Kai tells Natsume that he someone is chasing him every day.

Why don't you decide already? Which is more important to you? When Natsume finds out what Kai really is, that is what Natori asks him.