The film begins at Sannomiya Station on 21 September 1945, shortly after the end of World War II. A boy, Seita (清太), is shown dying of starvation. Later that night, having removed Seita’s body, a janitor digs through his possessions and finds a candy tin which he throws away into a nearby field. The spirit of Seita’s younger sister, Setsuko (節子), springs from the tin and is joined by Seita’s spirit as well as a cloud of fireflies. The spirits of Seita and Setsuko get into a train, heading in an unknown direction. Seita’s spirit then begins to narrate their story accompanied by an extended flashback of the final months of World War II.
The flashback begins in Kobe on 16–17 March 1945, with a fleet of several hundred American B-29 Superfortress bombers flying overhead. Setsuko and Seita, the two siblings, are left to secure the house and their belongings, allowing their mother, who suffers from a heart condition, to reach a bomb shelter. They are caught off-guard as the bombers begin to drop thousands of incendiary bomblets, which start huge fires that quickly destroy their neighborhood and most of the city. Although they survive unscathed, their mother is horribly burned and dies a short time later. Having nowhere else to go, Setsuko and Seita move in with a distant aunt, who allows them to stay but convinces Seita to sell his mother’s kimonos for rice. While living with their relatives, Seita goes out to retrieve supplies he had buried before the bombing. He gives them all to his aunt but hides a small tin of Sakuma fruit drops, which becomes a recurrent icon throughout the film. Their aunt continues to shelter them alongside her daughter and a local worker, but as food rations continue to shrink, she becomes increasingly resentful and openly remarks on how they do nothing to earn the food she cooks.