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.

Tanuma's father leaves on a trip and a strange youkai invades his house, spreading miasma that makes all the nearby youkai suffer. Natsume tracks it down and discovers that the noxious youkai was once a resident in an all-youkai village. A portal had opened for a short time during a human ceremony that he had taken his sister to watch. However, they became trapped in the human world, and his sister died. After returning to the old temple where the ceremonies were held, the portal opens and he returns home.

It's Shigeru's birthday and Touko has asked Natsume to buy some strawberry shortcakes to celebrate. However, Shibata, an old classmate of Natsume's, finds him and asks for his help. He remembered Natsume used to say weird things, so he wanted to know if a girl he's been seeing is real or not. When Natsume meets the girl, Murasaki, she seems normal. He reassures Shibata that she is a human. Natsume later has a vision that reveals her to be a tree youkai with intention to eat Shibata. Natsume tries to warn Shibata, he refuses to listen and accuses Natsume of lying. Natsume tries to talk to Murasaki, but she does not waver. It is then revealed that although she had initially planned to eat Shibata, she fell in love with him as they spent time together, and because her tree has been cut down, she will die soon anyway. Shibata receives a note from Murasaki just in time for the two of them to spend her last moments together.

Summer has arrived for Natsume and his friends in the school. After exams, Natsume, Sasada, Nishimura and Kitamoto go on a trip to an art museum. Upon his return, Touko reminisces about an old friend that she felt she'd wronged, this makes Natsume think back to his own turbulent childhood. In the present day, a youkai living in the branches of a tree thinks back to Natsume. She had been bored because no one could see her, and when she found out that Natsume could see youkai, she often scared him to be noticed. Both of them parted ways on bad terms. The story returns to Natsume in the present day, who makes a stop at his old neighborhood to visit the youkai. The youkai, who had isolated herself from humans, is relieved to see that Natsume is okay and has found a reason to smile. The episode ends with Natsume's thoughts, "If there is somebody that you wish to meet, then you are not alone anymore."

Natsume and Tanuma take shelter under a roof from the rain. As it turns out, the house belongs to Taki, and they work together to clean her warehouse where her grandfather studied youkai. Natsume accidentally breaks a seal that Taki's grandfather made to trap a dangerous kimono youkai. The three of them race around the house to find its misplaced limbs before the youkai does--its power will be returned upon completing its body. Natsume and Taki try to get the resident youkai to help, but they refuse. When the kimono youkai comes close to hurting Natsume, they come to the rescue. After Taki thanks them, they all reminisce about their fondness for Taki's grandfather and leave elsewhere.

Natsume accidentally bumps into a woman with blood covering her body. He follows the bloody footsteps that the woman left and discovers a small house. When he opens the door, he sees badly injured youkai. There is someone killing youkai for blood, and with the help of Natori, Natsume tracks down who he believes to be the murderer: Matoba. However, Matoba captures him.

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 is invited to go to a pottery classroom with Shigeru. It's being held in an inn where he once stayed. When he goes there, he meets an old friend: the young fox child he once saved.

Because of his poisonous arrow wound, Madara spends most of his time sleeping to heal. Without Sensei to protect him, Natsume has to remain constantly on guard. Especially since a strange stone seems to stir strange phenomena everywhere around him. To make things worse, it's the cultural festival and Natsume is appointed to serve the clients at the bazaar set by his class. But the pressure of keeping secrets from his friends is causing Natsume to break.

An event in the forest causes Tanuma to avoid Natsume the following days, which he becomes concerned about. Mirrors are mysteriously breaking around the school and one day Natsume catches Tanuma acting weirdly. It turns out that Tanuma has been possessed by a youkai looking for her mirror, which had been broken into pieces during a storm a few days before. Using him as a vessel until she reclaims her mirror, Natsume has no choice but to help her. The youkai warns that there may be others seeking the mirror.

Because of his possession, Tanuma is able to see the youkai around him and thus better understand how Natsume lives.

When a dangerous youkai from Natsume's past finds his current home, he comes down with a fever and dreams about his life right before moving in with the Fujiwaras.

Natsume spends time playing games with youkai he has befriended. He remembers games he was left out of as a child.

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 and Matoba talk, but when the conversation doesn't go the way he wants, Matoba orders Natsume to be put in a cell. Natsume escapes with the help of Nyanko-sensei. Along with his other demon companions, Natsume helps the monkey-masked demons living in the forest.

Natsume befriends a small fluffball youkai.

Yobiko, a youkai that can imitate the voices of others, sneaks into Natsumes' house and asks him to call out another youkai named Karikami. Long ago, Yobiko had been watching over a woman named Youko who was meeting with a man at a nearby shrine. One day the man stopped coming, due to an arranged marriage to another woman, so Yobiko decided to use his talent to talk to the girl. Eventually, he told her the truth about the man and ran away. When he came back to the shrine many years later, he found an old letter that had been sealed shut and wrinkled. Natsume and Yobiko later meet Karikami and after returning his name, Karikami restores the letter. Unable to read human letters, Yobiko asks Natsume to read it to him. Instead of a hateful message he was expecting, it is actually a letter of thanks for telling her the truth.

In the town Natsume used to live in, a girl recalls Natsume. She remembers his strange actions and wanted to understand him. Meanwhile, Natsume encounters a small Youkai which reminds him of the same girl and town.

Natsume is trapped in a bottle by a youkai to be offered to another named Omibashira. Nyanko-sensei transforms into Natsume and goes around his school to ask his friends about Omibashira, but gets Tanuma involved. Tanuma is attacked by one of the youkai that trapped Natsume and loses him, but as he runs through the forest looking for Natsume he finds a mansion behind the school. When Tanuma is suddenly able to see the youkai walking up the steps to the mansion, he is found out by a youkai with a bag over its head.

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.

Natori is tasked with the job of finding and breaking the seal of Houzukigami, a god that was to participate in the Moon-Splitting Festival done every 10 years against Fuzukigami, another god. The festival is used by the youkai around the mountains to determine whether the harvest would be bountiful that year or not. Without Houzukigami, the match would end in a default win for Fuzukigami, causing the land to become barren. Natori tries to find the seal but is surprised to find Natsume at the festival disguised as Houzukigami, having been asked by Houzukigami's servants to stand in for their god. The match to be the winner is to catch a beast that was released from a pot.

Houzukigami's servants tell Natsume to look for the real Houzukigami while they track down the beast. Joined by Natori, Hiiragi, Nyanko-sensei, and one of the servants, they look in a building by a waterfall. The beast suddenly appears and Natsume and Hiiragi are knocked off the deck of the building. After recuperating from being dragged down the river, they try to run back to the building but are caught in a trap by Fuzukigami's servants which was meant for the beast. While unconscious, one of the servants is able to pick up a human scent from "Houzukigami", making them wonder if it's truly the god or not.

Natsume is pretending to be the god Houzukigami, so the moon splitting festival will end with a victory and the mountain will not be ruined. Winning the contest will not be easy, but with help from Natori he will find the way.

Natsume looks back at a photo of his parents, and old wounds are reopened. Natsume is having a fun day with his friends, but all of a sudden he gets a phone call. The house Natsume used to live in with his father will be sold. How will Natsume handle all of this?

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.

Natsume, possessed by the youkai, thinks of an painful incident from his childhood involving the family he was living with at the time. The youkai offers to eat all his memories, so that he will no longer have to relive his pain.

Nyanko-sensei falls into a well and discovers that there is a barrier inside it, as well as Nanase, Matoba's assistant. She is looking for a certain stone with a youkai she had sealed in it, and tells Nyanko-sensei the story of how she met the youkai to pass the time.

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?

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 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.

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.

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.

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.

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.

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.

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.

The story of why Touko and Shigeru adopted Natsume.

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.