Takashi Natsume and his spirit companion, affectionately known as "Nyanko," are faithfully restoring balance by returning the spirits from the Book of Friends to their rightful owners. This book, inherited from Takashi's late grandmother, Reiko Natsume, is their guide. One day, on his way home from school, Takashi encounters a spirit named Monmonbou who remembers Reiko upon hearing Takashi's name. Intrigued by his grandmother's past, Takashi embarks on a journey to explore the mysterious town where Reiko once lived. Along the way, he meets Yorie Tsumura and her son Mukuo, who reveal more about Reiko's history. Meanwhile, Nyanko finds himself distracted while searching for food and discovers a peculiar "Spirit Seed," which sprouts overnight into a fruit tree. Giving in to his cravings, Nyanko indulges in the fruit, only to be shocked as he splits into three separate entities. To help Nyanko overcome this unexpected predicament, Takashi enlists the help of his friends and uncovers more secrets about the town in the process.