While the Second World War rages, the teenage Mahito, haunted by his mother's tragic death, is relocated from Tokyo to the serene rural home of his new stepmother Natsuko, a woman who bears a striking resemblance to the boy's mother. As he tries to adjust, this strange new world grows even stranger following the appearance of a persistent gray heron, who perplexes and bedevils Mahito, dubbing him the "long-awaited one."

Suzume, 17, lost her mother as a little girl. On her way to school, she meets a mysterious young man. But her curiosity unleashes a calamity that endangers the entire population of Japan, and so Suzume embarks on a journey to set things right.