A group of British schoolboys, aged 6-12, land on a deserted island in the middle of a war. Two of the boys, Ralph and Piggy, find a conch shell and use this to summon the other boys on the island. They meet Jack and his group of choir boys, and they elect Ralph as their leader. The group is mainly divided by age, as there are the littluns (around 6 years old) and the biguns (Ralph, Jack, and the boys closer to their age). There are no adults around, so the boys' only option is to fend for themselves and do what they need to in order to survive.
Ralph and Piggy together establish rules and priorities for the boys. Ralph emphasizes the need for a signal fire, which he believes will help them be rescued. However, the boys do not all agree about the fire being top-priority, as Jack and his crew mainly focus on hunting, which leads to conflict.
One day, one of the littluns mentions a beast on the mountain, and fear penetrates throughout the boys. While the beast was seen as figment of the littluns' imagination when the beat is initially mentioned, the looming spirit of the beast continues to cloud over the boys for the remainder of the novel.
One night, a parachutist falls from an onging battle in the sky, a result of the war occurring in the world. The parachutist falls onto the island and lands, tangled in the trees at the top of the mountain.
One night, Sam and Eric go up to the top of the mountain and they are frightened by the image of a beastly creature in the darkness, which is in reality just the parachutist tangled in the trees. The cries of Sam and Eric to the reminder of the group lead the boys to set out to find and eliminate the threat of the beast.
The boys go on their mission to find the beast, one that lasts the entire day. By the time the boys finally ascend the mountain, it is nightfall and the darkness is consuming. At the top of the mountain, Jack, Ralph, and Roger are horrified by the sight of an ape-like beast before them.
After returning to the beach, the boys have another meeting. The relations between the boys begins to go south, as Ralph and Jack continue to conflict against one another. Eventually, Jack takes off and convinces the hunters to follow his lead. The remaining boys—Ralph, Piggy, Simon, Sam, and Eric, and littluns—are within a separate group than the other boys. Ralph's tribe is focused on rescue still, although even Ralph sometimes forgets his mission. They primarily work to keep a fire readily going, while Jack leads his members to hunt and kill pigs.
Jacks group goes hunting one day and they make the decision to leave an offering of the meat for the beast in order to help protect themselves. Their offering was in the from of a pigs head placed upon a stick. Simon, who was hiding among the brush watches the whole ordeal and is disgusted with the actions of Jack's tribe and he begins to experience a delusion in which the pig head speaks to him. The pig's head comes across to Simon as the Lord of the Flies and he tells Simon that the beast is within all of the boys and cannot be escaped. Despite the voice of the Lord of the Flies telling Simon to stay away from the mountain, Simon climbs to the top, where he realizes that there never was any beast, only a dead man and a parachute.
When Simon returns to the beaches to tell the other boys of his important discovery, they are chaotically chanting and dancing around a feast. Simon's arrival does not stop the boys' hysteria and in a ferocious attack, Simon is killed, with the boys claiming him to be the beast.
The two tribes separate once again and Ralph's group begins to feel the guilt of the previous night's actions. The death of Simon weights heavily on their hearts and they begin to find excuses to justify their actions. Meanwhile, Jack plots against Ralph and his followers go with him to steal Piggy's glasses in the middle of the night. There was a struggle among the boys, but in the end, Ralph and his members are bloodied and without the means to create fire anymore.
Ralph and his group take a journey to where Jack and his followers were staying. The trip was in hopes of reasoning with Jack to take back the glasses, however the trip fails. Sam and Eric were tied up and forced to join Jack's tribe; Piggy gets crushed by a gigantic boulder that Roger pushes into him; Ralph must run for his life, as he is hunted by the boys he once called his friends; the conch breaks and disorder breaks loose.
Ralph hides in the forest, beside the Lord of the Flies, but he is forced to run towards the beach as the woods are taken over by flames set by Jack's tribe. Despite his exhaustion, Ralph manages to make it to the beach, where he is shocked to find a navy officer. While Ralph has finally reached safety, the idea of rescue is no longer as appealing and he begins to cry, remembering all the savage actions that had taken place on the island. Ralph knows that he can never go back to the way things were before the boys were stranded on the island.