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.

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 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...