Nyanko-Sensei wanders off from Natsume during a walk, and with the help of some of his fellow youkai, leads a pair of wandering children to the place they are searching for which they call, "mitsumonster."

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.

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...

While searching for Nyanko-sensei, Natsume gets invovled in a dangerous game of hide and seek.

Natsume encounters an old man who asks for help with getting home. The old man turns out to be a yokai who will soon disappear and he asks Natsume to help him to fulfill a promise that he had made.

A girl ventures into the woods to return a ring to an owl she helped, following the instructions he gave her in a dream. There she meets a strange boy and his talking cat who help her to find the owl.

Short 3D Nyanko-sensei animations bundled on BD/DVD's of the Zoku Natsume Yuujinchou series.

Short 3D Nyanko-sensei animations bundled on BD/DVD's of the Zoku Natsume Yuujinchou series.

Short 3D Nyanko-sensei animations bundled on BD/DVD's of the Zoku Natsume Yuujinchou series.

Short 3D Nyanko-sensei animations bundled on BD/DVD's of the Zoku Natsume Yuujinchou series.

Natsume has been busy, navigating between humans and Yokai when he coincidentally reunites with an old classmate, Yuki. It brings back painful memories of a certain Yokai. Meanwhile, Natsume also became acquainted with Yorie Tsumura, a woman in the memories of a Yokai whose name he had returned. Yorie knew much about Reiko, but now lived a peaceful life with her only son, Mukuo. Being with this family was comforting for Natsume, but apparently a mysterious Yokai has been lurking in their town.

On the way back from investigating, a "Yokai seed" that had latched itself to Nyanko Sensei drops into the Fujiwaras' garden and grows overnight into a fruit tree. When Nyanko Sensei eats a fruit that is somehow shaped like himself, he suddenly splits into three!

The film will be made up of two stories: "Ishi Okoshi" and "Ayashiki Raihousha." In "Ishi Okoshi," Natsume meets a small youkai called Mitsumi in a forest. Mitsumi is entrusted to wake up the divine youkai "Iwatetsu" from its deep slumber. Mitsumi weighs on Natsume's mind, so he sets out to help Mitsumi with his task.

In "Ayashiki Raihousha," a mysterious visitor appears in front of Tanuma. Nearly every day, the visitor visits Tanuma, talks to him a little, and then leaves. Natsume, who knows the visitor is a youkai, worries for Tanuma, but Tanuma enjoys these exchanges with the youkai. The youkai means no harm, but Tanuma's health slowly starts to deteriorate.