

As with its prequel, Zoku Natsume Yuujinchou is about Takashi Natsume, a boy who has had the ability to see youkai since he was young, and his bodyguard youkai Madara, nicknamed Nyanko-sensei. Natsume attempts to return names written in his "Book of Friends" (which he inherited from his grandmother Reiko) to youkai in his village. Throughout these adventures, he meets some youkai that are friendly, some that want to steal the Book, and some that want to kill him, as Natsume learns about himself and his relationship with these mysterious beings along the way. [Written by MAL Rewrite]






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 into 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 knows...
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 its 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. With her appearance at the school, circles resembling crop circles begin to appear. As Natsume tries to find out more about 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 Taki. He temporarily loses the ability to see youkai after being poisoned by the spirit. Will he be able to stop the youkai from eating Taki without his sight?
Natsume, Kitamoto and Nishimura take a trip to an old inn to spend some time doing their homework. Surrounding the inn there is a lake; in which is believed to live a mermaid.
From the day where 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 Nyanko Sensei try and return the picture to Miya, a shadow figure who accompanies the picture. But why can't they return it to Miya...?
Strange things start happening at Natsume's home, like Toukou's plants get destroyed, and a strange Youkai starts wandering around his house. Natsume then learns more about Reiko and her life in this town. He also learns how to get rid of the Youkai who's wandering around the house.