After her father's sudden death, eleven-year-old Momo Miyaura moves with her mother to a remote island in the Seto Inland Sea, leaving behind their former home in Tokyo. The only thing left from her father is an unfinished letter that begins with "Dear Momo," which leaves her with a lingering feeling of unease.
In this strange coastal town, Momo struggles to adjust to the old wooden houses, the calm countryside, and the mysterious shrines that dot the area. While exploring the attic of her new home, she finds an ancient picture book filled with illustrations of various youkai. Soon after, odd occurrences start happening around the village, and Momo meets three playful youkai spirits.
A Letter to Momo follows a young girl as she copes with her unfamiliar environment and tries to decode the puzzling message left behind by her father.