Episode 1 - Unchanging Form

Natsume continues to spend his days giving youkai back their names from the Book of Friends. One day, as he's heading home, he finds himself chased by a giant, rolling pot. The youkai in the pot insists that his grandmother Reiko stole a doll from her. When she threatens to hurt his family, however, he's forced to go out and find it. But would his kind, smiling grandmother Reiko really steal a doll from someone?

Episode 2 - Mischievous Rain

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?

Episode 3 - The Letter from the Exorcist

Natsume finds a letter addressed to him from Matoba. Walking in the forest, he loses it when an amateur exorcist seals a yokai in a pot. Noticing the weak seal, Natsume and Nyanko-sensei take it to Natori's condo to re-seal it. When Natsume returns home he sees Matoba and learns the letter was a request for Natsume to attend a meeting of strong exorcists to weed out the person who has been targeting exorcists.

Episode 4 - Shadow of Linked Chains

Matoba brings Natsume to one of the Matoba clan villas to attend the exorcist meeting. Natsume learns that a mask yokai called "Magatsumen" is controlling people and disguises himself as a shiki in order to test attendees if they have been possessed. By following a strange spring sound, Natsume finds the culprit behind the mask possessions and drives the yokai out. Matoba shoots the yokai with an arrow to exorcise it.

Episode 5 - It Must Not Be Bound

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.

Episode 6 - Soundless Valley

Natsume is chased by two yokai who cast a voice-sealing spell on him. A large bird yokai saves him and brings him to a valley before Nyanko-sensei finds him. Natsume regains his voice after the group of yokai attack him in his room, and then returns the bird yokai's name.

Episode 7 - Distant Festival Lights

Tanuma invites his friends to an inn run by his relatives. While sweeping outside, Tanuma is greeted by an old woman named Ito-san. Natsume learns that Ito-san is a yokai that serves the Mizunagi shrine by protecting the mountain festival. Ito-san has come into the inn because another yokai has stolen the festival's white mask and has disguised itself as an inn guest. Natsume finds the yokai who stole the mask for the festival's power, and Ito-san exorcises her. Ito-san warns Natsume to keep her identity a secret until after the festival is over so she can complete the festival. Natsume says he will tell no one she is a yokai so she can stay in this town as long as possible.

Episode 8 - A World Unbent

An episode depicting the story of Natori Shuuichi and Matoba Seiji when they were young. This episode shows Natori's family and his childhood of being able to see youkai, getting hated by his family and becoming an exorcist.

Episode 9 - Following a Narrow Path

The episode starts with Natsume being chased by a hairy youkai. He comes across a tiny mushroom youkai who tells him about a noble youkai named Shuon who was on a journey. Natsume helps the little youkai prepare for his meeting with the noble youkai. When they meet, however, the noble youkai warns the mushroom youkai that the path he takes is a narrow one and asks the little youkai to go back home. But then the little youkai realizes he need to become worthy in order to follow him. Another youkai, who appears to be one of the noble youkai followers, appears and gives a book to the mushroom youkai and tells him to complete the training to join Shoun-sama.

Episode 10 - Touko and Shigeru

The story of why Touko and Shigeru adopted Natsume.

Episode 11 - To the Ephemeral Ones

The mid-ranks show Natsume flowers at the top of a hill. Natsume later catches a cold and the mid-ranks go and get medicine for him, doing difficult chores for the yokai with the medicine. Amid Natsume's fever dreams are the memory of when he got sick as a child and he briefly talks to Reiko. With the medicine in hand, the mid-ranks give it to him and his fever goes down. They later learn the medicine doesn't work on humans and are disheartened as they wasted their time, but smile when Natsume thanks them for their efforts.

Episode 12 - Episode 12

Episode 13 - Episode 13