The movie of Natsume's Book of Friends 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 ghouls of Anteiku invaded the Aogiri's site in order to rescue Ken Kaneki who is being tortured. Due to provocation, he unleashed greater power enough to defeat Yamori. To become stronger, he decided to join Aogiri and left Anteiku. Ghoul investigators also making their moves by collecting information about the eye-patched ghoul - Ken Kaneki.