It soon shoes a flashback of Seita and Setsuko getting ready to go to the shelter because of a warned bomb raid. They leave home, and then the chaos starts. Bombs start to fall, people start to run, and gas starts to flow. Seita gets worried and starts to panic. He soon starts to run towards the shelter. They soon go to a nearby elemetary school where medical help is. Seita sees his mother terribly bandaged up. He is horrified by the sight of his mother's body. He worries because he knows that his mother already has heart problems, and that this would surely not be good for her. As he leaves the school, he doesn't tell Sieta about what happens to his mother. Instead he tells her that their mother is in a different hospital, but Setsuko sees her mother's ring with Seita and knows something is wrong. She cries, and Seita tries to take her mind off it by doing flips on the bars, but it doesn't work.
Seita and Setsuko are taken in by their aunt who starts to be nice at first, but gradually tends to be less caring, and more rude. She tells Seita that he is not helping, that he is just staying around not doing anything. When Setita and Setsuko's aunt wants to sell their mother's komonos, Setsuko cires and objects. There is nothing that she could do. Soon after, Seita and Setsuko get tired of their aunt, and move out.
After Seita and Setsuko move out, they soon find an empty bomb shelter. They use it as a place to stay. Dung their first nights stay, they gather fireflies to light up their new home. But the next morning, the fireflies die and fall to the ground. The next day Seita sees Setsuko burying the dead fireflies. He asks her why. She told him that this was the way they buried mom. Then Seitsa just stops. He grows his anger into his tears. He asked her who told her this, and Setsuko tells that auntie told her. Seita is furious, but all he could do is just cry. A few days later, Setsuko develops rashes and has occasional diarrhea. Seita takes her to the doctor and is dissapointed that the doctor cannot do anything. The doctor tells Setsuko that it is just malnutrition, and that she just needs food, but Seita knows that there is no food left. Desperate to save his sister, he tries to feed her food from any place he can find it. One night, Seita was caught stealing food from a nearby farmer. The farmer pulls Seita out of his garden and starts to abuse Seita. Seita tries to run away telling the farmer that the food was for his sick sister, and that he will never do it again. The farmer brings Seita to the police, but the police is more concerned about Seita's bruises more than the stolen food. He tells the farmer to leave, and starts to offer Seita some water. He comes back to the shelter, and rests. The next morning, he goes to the bank to withdraw some money, yet he also learnes that Japan has given up on the war. He is angry that his father has also drowned on a ship. He rushes back home to see Setsuko. He sees her resting but something is in her mouth. He saw that she is eating marbles and dirt. She must have been so hungry that she was desperate to eat anything. He takes the marble out of her mouth and starts to feed her watermelons. After eating, she soon goes to sleep. She never woke up.
Seita is emotionally powerless. He has just lost everyone that was close to him. He creamates Setsuko and heads off to the station. He rests there until his soul has finally left his body.
The last scene shows Setsuko and Sieta's ghost sitting on the bench. Even though Seita and Setsuko are not with each other physically, their souls wander off together though the night, like fireflies in the field.
