

Takahata explained that any wartime story, whether animated or not animated, "tends to be moving and tear-jerking", and that young people develop an "inferiority complex" where they perceive people in wartime eras as being more noble and more able than they are, and therefore the audience believes that the story has nothing to do with them.

Isao Takahata said that he was compelled to film the short story after seeing how the main character, Seita, "was a unique wartime ninth grader". After seeing the storyboards, Nosaka concluded that it was not possible for such a story to have been made in any method other than animation and expressed surprise in how accurately the rice paddies and townscape were depicted. Nosaka expressed surprise when an animated version was offered. He also argued that contemporary children would not be able to convincingly play the characters. Nosaka argued that "it was impossible to create the barren, scorched earth that's to be the backdrop of the story". Grave of the Fireflies author Akiyuki Nosaka said that many offers had been made to make a live-action film adaptation of his short story. Surrounded by fireflies, they rest on a hilltop bench overlooking present-day Kobe. Their spirits later arrive at their destination, healthy and happy. They board a ghostly train and, throughout the journey, look back at the events leading to Seita's death. Setsuko's ashes spread out, and her spirit springs from the tin and is joined by Seita's spirit and a cloud of fireflies. The janitor sorts through Seita's possessions and finds the candy tin, which he throws into a field. A janitor is tasked with removing the bodies before the arrival of the Americans. Later on 21 September, shortly after the end of World War II, Seita is malnourished and lying down in a train station at Sannomiya surrounded by other malnourished people.

He carries her ashes in the candy tin along with his father's photograph. Seita cremates Setsuko's body and her stuffed doll in a straw casket. She later dies as Seita finishes preparing the food. Seita returns to Setsuko with food, but finds her dying. After doing so, he becomes distraught when he learns that Japan has surrendered, and that his father, an Imperial Japanese Navy captain, is most likely dead, as most of Japan's navy has been sunk. Desperate, Seita withdraws the last of the money in their mother's bank account. When Setsuko falls ill, a doctor explains that she is suffering from malnutrition. The policeman realizes Seita is stealing because he and Setsuko are hungry and decides to release Seita. As they run out of rice, Seita steals from farmers and loots homes during air raids, for which he is beaten and sent to the police. She buries them in a grave, asking why they and her mother had to die. The next day, Setsuko is horrified to find that the insects have died. They release fireflies into the shelter for light. Seita and Setsuko decide to leave the aunt's home after excessive insults, and they move into an abandoned bomb shelter. Seita uses some of his mother's money in the bank to buy supplies, but eventually, the aunt becomes resentful of the children, deeming them unworthy of earning her food. The aunt convinces Seita to sell his mother's silk kimono for rice as rations shrink and the number of refugees in the house grows. Seita and Setsuko move in with a distant aunt, and Seita retrieves supplies he buried before the bombing and gives everything to his aunt, save for a tin of Sakuma drops. Seita conceals their mother's death from Setsuko in an attempt to keep her happy, which she later learns of despite Seita's efforts. They escape unharmed, but their mother dies from severe burns. In 1945, teenager Seita and his younger sister Setsuko's house is destroyed in a firebombing along with most of Kobe. Incendiary bombs being dropped onto Kobe, the setting of the film
