High schoolers Mitsuha and Taki are complete strangers living separate lives. But one night, they suddenly switch places. Mitsuha wakes up in Taki’s body, and he in hers. This bizarre occurrence continues to happen randomly, and the two must adjust their lives around each other.

Due to an unusual ability to see strange creatures called youkai, Takashi Natsume has never fit in. Over time, he has accepted that no one would ever believe him and has closed himself. When Natsume accidentally breaks an intangible barrier, he frees Madara—a mighty spirit in the form of a lucky cat. Madara notices that Natsume bears a remarkable resemblance to his late grandmother Reiko Natsume, an outcast girl who created the Book of Friends. It is now in Natsume's possession. With no interest in its powers, Natsume decides to keep the book for the sake of his grandmother's memories and to protect it from scheming youkai. Therefore, he makes a deal with Madara: he will hand him the book once his time is up, and in turn, Madara will act as Natsume's unofficial bodyguard. With his newfound goal of freeing those Reiko had sealed, Natsume's relationship with both youkai and humans slowly begins to improve.

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!