In the midst of a raging war, a plane evacuating a group of English boys from Britain is shot down over a deserted tropical island. Marooned, the boys set about electing a leader and finding a way to be rescued. They choose Ralph as their leader, and Ralph appoints Jack to be the leader of the hunters. Ralph, Jack, and Simon set off on an expedition to explore the island. When they return, Ralph declares that they must light a signal fire to attract the attention of passing ships. The boys begin to do so, using the lens from Piggy's eyeglasses to ignite dead wood, but they are more interested in playing than in paying close attention to their duties, and the fire quickly ignites the forest. A large swath of dead wood burns out of control. One of the youngest boys disappears, presumably having burned to death.
At first, the boys enjoy their life without grown-ups. They splash in the lagoon and play games, though Ralph complains that they should be maintaining the signal fire and building huts for shelter. The hunters have trouble catching a pig, but Jack becomes increasingly preoccupied with the act of hunting. One day, a ship passes by on the horizon, and Ralph and Piggy notice, to their horror, that the signal fire has burned out; it had been the hunters' responsibility to maintain it. Furious, Ralph accosts Jack, but the hunter has just returned with his first kill, and all the boys seem gripped with a strange frenzy, reenacting the chase in a kind of wild dance. When Piggy criticizes him, Jack hits him across the face.
Ralph blows the conch shell used to summon the boys and reprimands them in a speech intended to restore order. Yet there is a larger, more insidious problem than keeping the signal fire lit and overcoming the difficulties of hunting: the boys have started to become afraid. The littlest boys (known as "littluns") have been troubled by nightmares from the beginning, and more and more boys now believe that there is some sort of beast or monster lurking on the island. At the meeting, the older boys try to convince the others to think rationally: if there were a monster, where would it hide during the daytime? One of the littluns suggests that it hides in the sea, a proposition that terrifies the whole group.
Not long after the meeting, an aircraft battle takes place high above the island. The boys are sleeping, so they do not notice the flashing lights and explosions in the clouds. A parachutist drifts to earth on the signal fire mountain. He is dead. Sam and Eric, the twins responsible for watching the fire at night, have fallen asleep, so they do not see him land. But when they wake up, they see the enormous silhouette of his parachute and hear the strange flapping noises it makes. Thinking the beast is at hand, they rush back to the camp in terror and report that the beast has attacked them.
The boys organize a hunting expedition to search for monsters. Jack and Ralph, who are increasingly at odds, travel up the mountain. They see the silhouette of the parachute from a distance and think that it looks like a huge, deformed ape. The group holds a meeting, at which Jack and Ralph tell the others of the sighting. Jack says that Ralph is a coward and that he should be removed from office, but the other boys refuse to vote him out of power. Jack angrily runs away down the beach, calling all the hunters to join him. Ralph rallies the remaining boys to build a new signal fire, this time on the beach instead of on the "monster's" mountain. They obey, but before they have finished the task, most of them have slipped away to join Jack.
Jack declares himself the leader of this new tribe, and organizes a hunt and violent, ritual slaughter of a sow to solemnize the occasion. They then decapitate the sow and place its head on a sharpened stake in the jungle as an offering to the beast. Encountering the bloody, fly-covered head, Simon has a terrible vision, during which it seems to him that the head is speaking. The voice, which he imagines to belong to the Lord of the Flies, says that Simon will never escape him, for he exists within all men. Simon faints; when he wakes up, he goes to the mountain, where he sees the dead parachutist. Understanding then that the monster does not exist externally but rather within each individual boy, Simon travels to the beach to tell the others what he has seen. But they are in the midst of a chaotic revelry—even Ralph and Piggy have joined Jack's feast—and when they see Simon's shadowy figure emerge from the jungle, they fall upon him and kill him with their bare hands and teeth.
The following morning, Ralph and Piggy discuss what they have done. Jack's hunters attack them and their few followers, stealing Piggy's glasses in the process. Ralph's group travels to Jack's stronghold, called Castle Rock, in an attempt to make Jack see reason. But Jack orders Sam and Eric tied up and fights with Ralph. In the ensuing battle, one boy, Roger, rolls a boulder down from the mountain, killing Piggy and shattering the conch shell. Ralph barely manages to escape a torrent of spears.
All night and throughout the following day, Ralph hides and is hunted like an animal. Jack has the other boys ignite the forest in order to smoke him out of his hiding place. Ralph discovers and destroys the sow's head in the forest; eventually, however, he is forced out onto the beach, where he knows the other boys will soon arrive to kill him. Ralph collapses in exhaustion, but when he looks up, he sees a British naval officer standing over him. His ship noticed the blazing fire now raging in the jungle. The other boys reach the beach and stop in their tracks at the sight of the officer. Amazed at the spectacle of this group of bloodthirsty, savage children, the officer asks Ralph to explain. Ralph is overwhelmed by the knowledge that he is saved, but thinking about what has happened on the island, he begins to weep. The other boys begin to sob as well. The officer turns his back so that the boys may regain their composure.