Natsume travels to an inn for a study session with the rest of his class. While he's there, a flood washes away a local shrine. The shrine is said to house three masks, but Natsume can see four...

Natori is trying to find information on Natsume and his book of friends. Meanwhile, Natsume visits his house to deliver some of Touko's homemade jam. But this is the start of an adventure...

The youkai hold a party to celebrate Natsume. Things get out of hand when they ask Natsume for a human game, and he suggests Shadow Tag. When Nyanko-sensei becomes "it", he starts stomping youkai left and right. And then Misuzu-sama, the 100 foot tall youkai, shows up...

After Natsume returned Amana's name, she accused him of stealing her ring. He has three days to find and return it before she burns down his house. To make matters worse, the ring is trapped in the hair of a migratory youkai, and Nyanko-sensei is unable to use his powers.

Natsume gets a call from a relative: his parents home is being sold. He tells himself that it doesn't matter, and that he's forgotten his past. But he's not nearly as over it as he thinks...

Natsume's friends reflect on how they met him, and the difference he made in their lives. He's found a home, and he means a lot to the people who live there.

Natsume meets a youkai named Gomochi, who has come in search of Reiko. The youkai has a message for Reiko, and wants to thank her for a favor she did him long ago. In hearing his story, Natsume comes to learn more about his mysterious grandmother.

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, 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.

Natsume's town is visited by a stonewasher: a powerful magical being capable of purifying tainted rocks. The stonewasher is looking for its lost student, and turns to Natsume for help.

Natsume gets a call from his old "friend" Shibata, who he once helped with a youkai problem. Shibata wants him to come visit, and Natsume reluctantly agrees. He and Tanuma pay Shibata a visit, and have a pleasant chat at a park. But when Shibata mentions a local haunted house, Natsume finds his visit has turned into more than he expected...

Natsume watches a movie starring Natori, and when he's done he finds one of Natori's paper dolls. The doll is soaked and the text on it is impossible to read, and Natsume becomes concerned for Natori's safety. He travels to the location that's just barely legible on the doll, and finds a young woman whose home is haunted by not one, but three youkai.

Natsume is on his way home when he finds a letter on the ground. The letter seems to belong to a nearby man, who asks Natsume to take him to his school. The man is actually a youkai, who was once deeply involved with a human girl. He cut the relationship off, but the girl isn't ready to give up...

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 it's 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!

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...?

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.

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...

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?

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

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.

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.

Natsume finds that Tsukiko's home is haunted by not one, but three separate youkai, each with its own motivations. One wants to protect Tsukiko's father, and the other two... Natori wants to exorcise them and protect Tsukiko, but Natsume wants to find some way to protect them. Is there a peaceful solution?

Natsume meets a popular actor named Natori Shuuichi who can also see spirits, and has a side job as an exorcist.

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

There is a new girl in school Taki Tooru. And with her appearance at school comes these strange circles in the ground. Much like UFO circles. As Natsume tries to figure out 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.