Natsume discovers that the heirloom "Book of Friends" that his grandmother, Reiko, gave him possesses the names of the spirits she defeated and bound to her will. Assisted by a cat whom Natsume addresses as Nyanko-Sensei (lit. Master Little Meow), Natsume aims to return all of the names to their rightful owners.

Natsume is visited by the village's local god who is currently fading because of the lack of devotees.

Natsume is implored to help spirits who are currently being exorcised. He finds a kindred spirit in Tanuma, a boy who also senses spirits although not as powerful as Natsume.

Natsume's secret is found out by Sasada, the class president, during the "Trial of Courage." She asks for his help to find the spirit that lives in the abandoned school. Natsume denies the fact that he can see anything, but she won't take no for an answer. Meanwhile, the spirit, Shigure, captures the rest of their school mates, in fury of the school being torn down...

Natsume comes across an old ticket in Reiko's belongings and decides to go to the abandoned train station to see why she kept it. There, he meets a slow witted spirit named Santo, who was waiting for Reiko the entire time to go Kiriganuma, to see and make up with his friend, Mikuri, but the trip isn't as easy as it first seems...

Natsume goes to a dam and finds a town that had been submerged in water. Just then, Natsume gets possessed by a yokai and falls unconscious.

Natsume goes to a hot spring for a school trip, with an errand from Shigeru to pick up teacups from a near by pottery. While there he meets and helps a little fox spirit, who quickly grows attached to him.

Natsume meets a spirit who used to be friends with a man who could also see spirits, but one day lost this ability.

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

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

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

Natsume is cursed by an evil spirit which is sealed to a tree, not wanting to trouble his adopted family, he decided to run away from home.

Tanuma finds out Nyanko-Sensei is a spirit. Tanuma and Natsume enjoy the autumn festival and previous acquaintances are seen again.

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 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!

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. 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.

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?

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.

One day, Natsume finds a yokai named Kagejawan running around near his home, which he soon learns means disaster is about to strike.

Natsume is accosted by a spirit who asks for her brother's name back. She says that both of them have come from the village of floating spring, a paradise sealed off from the land of men. Meanwhile, the local Youkai are happy that the local priest is no longer in his temple. Natsume worries for his friend Tanuma, the priest's son, but isn't sure what to say...

Natsume is approached by someone he knew from elementary school. He wants nothing to do with them, but they threaten to reveal his secret: that he can see Youkai, if he doesn't come along with them. He reluctantly goes with them, and is taken to meet a strange girl...

Midterms are over, and Natsume leaves on a trip with Nishimura, Kitamoto, and Sasada. He realizes that the scenery he's viewing from the train is from one of the places he grew up in, when he was passed around from one family to the next. He'd thought he didn't have any good memories of the time, but then he remembers what happened when he lived there...

Natsume helps clean the stoeroom at Taki's house with Tanuma. He realizes that one of the kimonos that her grandfather, who researched youkai, used to ward off demons was missing, but decides not to tell them so they won't be scared. But that kimono was an old doll youkai, who was trying to recover its body which was torn apart when her grandfather sealed it

There is something killing Youkai and draining them of their blood. Natsume can't help but investigate and runs into old friends.

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.

Without Sensei to protect him, Natsume has to remain constantly on guard. But the pressure of keeping secrets from his friends is causing Natsume to break.

After a brief incident in the forest, Tanuma has become distant to Natsume like he is avoiding something. In the meantime, there is something breaking glass around the school.

Tanuma is experiencing how Natsume lives every day. While Natsume and the youkai gain an understanding.

A youkai from Natsume past has found him and memories of living with relatives before the Fujiwaras are explored.

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...

Natsume is jumped by a group of Youkai trying to steal the Book of Friends for their master. Once captured, Natsume discovers that an old problem is back in a big way.

Natsume, now trapped in the mansion, is trying to keep the Monkey Mask youkai from revealing the Book of Friends to Matoba. While Hinoe and Misuzu attempt to find the strange youkai's master.

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 is at home early one evening when he hears a knock on the door. He sees Tohko outside, asking to be let in. But when he opens the door, there's nobody there, and a gust of wind rushes past. Another Youkai is after the book of friends!

An old classmate Yuriko, remembers her time watching Natsume and how he was a little weird. A clingbug from Natsume's past reminds him of the time he spent running from a youkai with a grudge.

Natsume overhears whispers that a powerful youkai is reviving, later that evening he is trapped in a bottle as an offering. Humans can't see or hear him, so Nyanko-sensei decides to help the “best” way he can…

Natsume's greatest fear has come true. Someone not involved in the world of youkai is hurt because of him. Natori needs Natsume to regain his composure or they will be eaten by Omibashira!

Natsume is walking home one day when he's accosted by a flying Tengu, who lifts him up into the sky! Meanwhile, Nyanko-sensei is stuck in a well, where Nanase tells him a story about how she learned to never get close to a youkai.

Every 10 years the followers of Houdzuigami and Fudzukigami have a battle to determine the fate of the land. Natsume is approached by the followers of Houdzukigami to act as their missing god. Natori has been given the job of finding the missing god or seal Fuduzkigami before he wins.

While being swept down the river, Natsume managed to feel the presences of Hudzuki-gami. Natori must make the choice to follow Natsume instincts or seal Fudzuki-gami.

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 is going home for the last time, but first he must stop by his relative's house to get the key. But he is cautious, as inside is a youkai that tormented Natsume, and a girl that has always resented him.

Natsume is possessed by a spirit. Obsessed with returning home, he remembers the events that occured just after his father's death.

Natsume continues to spend his days giving back Youkai 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 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.

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 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.

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.

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...

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...

Touko and Shigeru are the kind elderly couple who took in Natsume when no one else would. But what were they like before they let Natsume move in?

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 helps a youkai out of a pot, and as a "reward", is made young again. But Natsume is already young, and making him younger just confuses him and addles his memories. When he doesn't know who to trust, will he have the strength to know who his real friends 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.

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 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...

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...