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 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'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.

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 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's group searches the Hakozaki mansion for the study. But other forces want the powerful magics contained within, and Natsume doesn't want them to have it...

While on the run from a fearsome youkai, Natsume accidently sits on a tiny mushroom youkai. The mushroom youkai is incensed, as it has a meeting with a 'noble person' later in that day. It insists on Natsume helping it prepare for its meeting with this 'noble person', and Natsume finds himself drawn into the strange story of its past...

Natsume receives a letter from Matoba, an exorcist whom he's had unpleasant dealings with in the past. The world of exorcists is a dangerous place lately, and Matoba wants Natsume's help. Natsume wants to refuse, but Matoba threatens to reveal Natsume's powers to his adopted family, which would spell the end of his peaceful life.

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...

An inexperienced exorcist tries and fails to completely seal a youkai near Natsume's school. Natsume decides to take the pot the youkai is sealed in to Natori, in hopes that it can be disposed of properly. While he's there, he learns that there is an ongoing feud between exorcists lately, and that one exorcist in particular is attacking his rivals. When Natsume gets home, he finds that Matoba, another exorcist who's tried to take advantage of him in the past, wants his help dealing with just that particular problem...

Natsume's friend Taki lives in a house filled with traps and mazes for youkai. She can't see the youkai herself without the aid of a special circle, but she can hear them when they're trapped in her house. She saves one of them, but it refuses to leave her home. Natsume suspects that there may be danger involved, and visits her to make sure that everything is okay.

Natsume and his friends go to a distant hot springs to help with the renovations. When he arrives, he meets an old friend of Tanumas, but he quickly gets caught up in local youkai trouble. Tanuma's old friend is actually a youkai, and she threatens terrible things if Natsume reveals her secret.

Natsume has come down with a cold after adventuring in the hills. All of his friends, both human and youkai, do their best to make him feel better. As he lies in bed, he begins to realize how much the people around him care for him, and how valuable the bonds he's established are.

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.

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...

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.

Natsume arrives at the exorcist meeting to help smoke out the youkai that Matoba wants to find. But he quickly discovers that the situation is more complicated than it first seemed. The youkai is capable of replicating itself to possess targets, and no one but Natsume is able to see who is possessed. Natsume and Nyanko-sensei search the halls, still unsure if they even want to be there.

Natori's family has always been exorcists... until they lost the abililty to see youkai. After generations of fearing the youkai's revenge, Natori is suddenly born with the ability to see them. His family doesnt want anything to do with his powers, though, and he's left to figure out how to live on his own. His life changes when he meets a young Matoba at an exorcist gathering, and the two of them end up hunting a powerful youkai together...

Natsume is possessed by a sick koto player, whose friend wants her to be able to play one last time.

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?