Summer has arrived for Natsume and his friends in the school. After exams, Natsume, Sasada, Nishimura and Kitamoto go on a trip to an art museum. Upon his return, Touko reminisces about an old friend that she felt she'd wronged, this makes Natsume think back to his own turbulent childhood. In the present day, a youkai living in the branches of a tree thinks back to Natsume. She had been bored because no one could see her, and when she found out that Natsume could see youkai, she often scared him to be noticed. Both of them parted ways on bad terms. The story returns to Natsume in the present day, who makes a stop at his old neighborhood to visit the youkai. The youkai, who had isolated herself from humans, is relieved to see that Natsume is okay and has found a reason to smile. The episode ends with Natsume's thoughts, "If there is somebody that you wish to meet, then you are not alone anymore."

Because of his poisonous arrow wound, Madara spends most of his time sleeping to heal. Without Sensei to protect him, Natsume has to remain constantly on guard. Especially since a strange stone seems to stir strange phenomena everywhere around him. To make things worse, it's the cultural festival and Natsume is appointed to serve the clients at the bazaar set by his class. But the pressure of keeping secrets from his friends is causing Natsume to break.

When a dangerous youkai from Natsume's past finds his current home, he comes down with a fever and dreams about his life right before moving in with the Fujiwaras.

Yobiko, a youkai that can imitate the voices of others, sneaks into Natsumes' house and asks him to call out another youkai named Karikami. Long ago, Yobiko had been watching over a woman named Youko who was meeting with a man at a nearby shrine. One day the man stopped coming, due to an arranged marriage to another woman, so Yobiko decided to use his talent to talk to the girl. Eventually, he told her the truth about the man and ran away. When he came back to the shrine many years later, he found an old letter that had been sealed shut and wrinkled. Natsume and Yobiko later meet Karikami and after returning his name, Karikami restores the letter. Unable to read human letters, Yobiko asks Natsume to read it to him. Instead of a hateful message he was expecting, it is actually a letter of thanks for telling her the truth.

Natsume looks back at a photo of his parents, and old wounds are reopened. Natsume is having a fun day with his friends, but all of a sudden he gets a phone call. The house Natsume used to live in with his father will be sold. How will Natsume handle all of this?

Natsume, accompanied by Nyanko-sensei, set out to visit his old home. He visits a relative to pick up the key to the house, but is being followed by a youkai who wants him to draw a mouth for it. He leads the youkai away from the home of his relatives and Nyanko-sensei drives it away. When the two get back on track to finding the house, Natsume is suddenly attacked by the youkai and becomes lost in old memories.

Natsume, possessed by the youkai, thinks of an painful incident from his childhood involving the family he was living with at the time. The youkai offers to eat all his memories, so that he will no longer have to relive his pain.

During a winter walk, Natsume meets a snowman yokai who is searching for something she lost but can't seem to recall and decides to help her despite not knowing what exactly she was looking for.

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?

Tanuma invites his friends to an inn run by his relatives. While sweeping outside, Tanuma is greeted by an old woman named Ito-san. Natsume learns that Ito-san is a yokai that serves the Mizunagi shrine by protecting the mountain festival. Ito-san has come into the inn because another yokai has stolen the festival's white mask and has disguised itself as an inn guest. Natsume finds the yokai who stole the mask for the festival's power, and Ito-san exorcises her. Ito-san warns Natsume to keep her identity a secret until after the festival is over so she can complete the festival. Natsume says he will tell no one she is a yokai so she can stay in this town as long as possible.

Natsume encounters a pair of youkai who make cups that turn sake delicious. Their power is waning, and they've come to a spring that's said to restore spiritual energy. But the spring is occupied by a monster...

Natsume helps a rock washer look for his apprentice who has stopped writing him.

Natsume is surprised when a youkai comes to seek Reiko in gratitude. Years ago, the youkai's to-be-bride received freedom from her help, and now is about to be wed. They invite Natsume to the wedding.