Gen Nakaoka and his family live in Hiroshima, Japan during the final days of World War II. The family struggles with food shortages and constant air-raid warnings. Kimie Nakaoka is pregnant and malnourished, and Gen's sister Eiko Nakaoka helps with the housework. Daikichi Nakaoka and his son Shinji Nakaoka work in the family’s wheat field, trying to find sustenance for Kimie. As the war drags on, Daikichi and Kimie sense the fighting isn’t going well, and they wonder why Hiroshima has somehow been spared the air strikes that devastated other cities.
On August 6, 1945, Gen and a friend reach the school just as a lone B-29 roars overhead and drops an atomic bomb, razing the city. The friend is killed in the blast, and Gen is buried under rubble yet somehow survives. He finds his mother attempting to rescue their family, who are buried alive beneath their burning home, but Daikichi urges Gen to look after his mother and the baby. Daikichi, [Eiko Nakaoka], and [Shinji Nakaoka] burn to death as Kimie briefly suffers a mental breakdown. With the help of a neighbor, the two find a safer place where Kimie gives birth to a baby girl, Tomoko. The city is then coated in Black rain, the fallout from the bombing.
Gen spends the next days scouring for food. He discovers that soldiers are distributing rice, but the men are also gathering bodies to burn in mass graves. He carries a radiation-poisoned soldier to a makeshift hospital, where the soldier dies. Gen manages to loot a few bags of intact rice from a ration warehouse and brings them to his mother, together with some fresh vegetables. Kimie notices bald patches on Gen’s head, recalling the soldier’s death from an unknown illness, and Gen is struck by the memory, triggering a mental breakdown.
A few days later, on August 9, another atomic bomb drops on Nagasaki after Japan refuses to surrender following an ultimatum from the United States. On August 15, Gen and Kimie dig up the remains of their family from their former home and learn from a nearby family that Japan has surrendered, though their prayers for peace come too late. They take refuge in a makeshift shack and try to subsist on meager rations. A small boy, Ryuta, tries to steal their rice, but Gen catches him and is startled by Ryuta’s resemblance to Shinji. They decide to take Ryuta in after learning he was orphaned by the bombing.
In the days that follow, Gen and Ryuta search for food as Tomoko grows malnourished. A man offers them a job tending to his ill-tempered brother Seiji, paying 10 yen a day, but the boys grow weary of mistreatment and quit. Seiji pleads with them to return, grateful that they treated him like more than a rotting corpse. Gen tells Ryuta to tell his mother where they are, and he spends the night with the man, which rekindles his love of painting. The brother then pays them 100 yen and they head out to find milk for Tomoko. When they return, they discover that Tomoko has died.
Weeks later, Gen and Ryuta notice that wheat is beginning to grow again, offering a glimmer of renewed hope. They set a paper boat lantern adrift on the river, and together they watch it sail toward the sunset, holding on to the quiet possibility of a better tomorrow.
