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...

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...

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

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.

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 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.

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 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

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.

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

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.

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.

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.

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.

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'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 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...

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 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.

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'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.