A twelve-year-old boy, Mahito, loses his mother in an air raid on Tokyo during the 1943 war. After her death, her father buys an aircraft ammunition factory and marries Natsuko, his late wife's younger sister. Unfortunately, the entire family is soon forced to flee to the countryside. A young boy has difficulty adapting to life in a new place. He is still struggling with the death of his mother, is bullied at school, and his relationship with Natsuko is stressful because she is pregnant and expecting a child. Mahito also encounters a mysterious gray heron that torments him regularly.