Tokyo, near the end of World War II in the Pacific. 11 year old Mahito loses his mother in a fire, and takes refuge with his father in his mother’s hometown. They move into an old mansion on a large estate, which also includes a secluded tower that has become a nesting spot for a gray heron. Mahito struggles with complex feelings toward his father, who runs a factory supplying the war effort, and his new stepmother Natsuko, who happens to be his mother’s younger sister. To make matters worse, he becomes alienated at school. Mahito was told that the tower was built by his mother’s granduncle, who eventually disappeared inside it, never to be seen again.

One day, Natsuko suddenly goes missing, so Mahito ventures into the tower to look for her. Led by the gray heron, he unwittingly ends up embarking on an odyssey into another world. Mahito finds himself in a bizarre realm where the living and the dead exist side by side. As he encounters its astonishing inhabitants, he comes to learn of the secrets of the world.