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.

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.

While out on an errand for Touko-san, Natsume is caught by two hairy-ball youkai, who influence him with dark energy and make him unable to speak. He is rescued by a bird-like youkai name Hidaka, who takes him to her "nest" in an abandoned valley.

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.