Mahito Maki, a twelve-year-old boy in wartime Japan, loses his mother to a hospital fire and relocates with his father Shoichi to a rural estate, where his father has married Natsuko, his late mother's younger sister. A gray heron begins visiting Mahito with promises about his mother. When Natsuko vanishes into an ancient tower on the estate grounds, Mahito follows the bird inside and enters a realm where the living and the dead share the same space.