During an unnamed time of war, a plane carrying a group of British schoolboys is shot down over the Pacific. The pilot of the plane is killed, but many of the boys survive the crash and find themselves deserted on an uninhabited island, where they are alone without adult supervision. The first two boys introduced are the main protagonists of the story: Ralph is among the oldest of the boys, handsome and confident, while Piggy, as he is derisively called, is a pudgy asthmatic boy with glasses who nevertheless possesses a keen intelligence. Ralph finds a conch shell, and when he blows it the other boys gather together. Among these boys is Jack Merridew, an aggressive boy who marches at the head of his choir. Ralph, whom the other boys choose as chief, leads Jack and another boy, Simon, on an expedition to explore the island. On their expedition they determine that they are, in fact, on a deserted island and decide that they need to find food. The three boys find a pig, which Jack prepares to kill but finally balks before he can actually stab it.
When the boys return from their expedition, Ralph calls a meeting and attempts to set rules of order for the island. Jack agrees with Ralph, for the existence of rules means the existence of punishment for those who break them, but Piggy reprimands Jack for his lack of concern over long-term issues of survival. Ralph proposes that they build a fire on the mountain which could signal their presence to any passing ships. The boys start building the fire, but the younger boys lose interest when the task proves too difficult for them. Piggy proves essential to the process: the boys use his glasses to start the fire. After they start the fire, Piggy loses his temper and criticizes the other boys for not building shelters first. He worries that they still do not know how many boys there are, and he believes that one of them is already missing.
While Jack tries to hunt pigs, Ralph orchestrates the building of shelters for the boys. The smallest boys have not helped at all, while the boys in Jack's choir, whose duty is to hunt for food, have spent the day swimming. Jack tells Ralph that he feels as if he is being hunted himself when he hunts for pigs. When Simon, the only boy who has consistently helped Ralph, leaves presumably to take a bath, Ralph and Jack go to find him at the bathing pool. But Simon instead is walking around the jungle alone. He finds a serene open space with aromatic bushes and flowers.
The boys soon settle into a daily pattern on the island. The youngest of the boys, known generally as the "littluns," spend most of the day searching for fruit to eat. When the boys play, they still obey some sense of decency toward one another, despite the lack of parental authority. Jack continues to hunt, while Piggy, who is accepted as an outsider among the boys, considers building a sundial. A ship passes by the island but does not stop, perhaps because the fire has burned out. Piggy blames Jack for letting the fire die, for he and his hunters have been preoccupied with killing a pig at the expense of their duty, and Jack punches Piggy, breaking one lens of his glasses. Jack and the hunters chant, "Kill the pig. Cut her throat. Bash her in" in celebration of the kill, and they perform a dance in which Maurice pretends to be a pig and the others pretend to attack him.
Ralph becomes concerned by the behavior of Jack and the hunters and begins to appreciate Piggy's maturity. He calls an assembly in which he criticizes the boys for not assisting with the fire or the building of the shelters. He insists that the fire is the most important thing on the island, for it is their one chance for rescue, and declares that the only place where they should have a fire is on the mountaintop. Ralph admits that he is frightened but says that there is no legitimate reason to be afraid. Jack then yells at the littluns for their fear and for not helping with hunting or building shelters. He proclaims that there is no beast on the island, as some of the boys believe, but then a littlun, Phil, tells that he had a nightmare and when he awoke saw something moving among the trees. Simon says that Phil probably saw Simon, for he was walking in the jungle that night. But the littluns begin to worry about the beast, which they conceive as a ghost or a squid. Piggy and Ralph fight once more, and when Ralph attempts to assert the rules of order, Jack asks rhetorically whether anyone cares about the rules. Ralph in turn insists that the rules are all that they have. Jack then decides to lead an expedition to hunt the beast, leaving only Ralph, Piggy and Simon behind. Piggy warns Ralph that if Jack becomes chief, the boys will never be rescued.
That night, during an aerial battle, a pilot parachutes down the island. The pilot dies, possibly on impact. The next morning, as the twins Sam and Eric are adding kindling to the fire, they spot the pilot and mistake him for the beast. They scramble down the mountain and wake up Ralph. Jack calls for a hunt, but Piggy insists that they should stay together, for the beast may not come near them. Jack claims that the conch is now irrelevant. He takes a swing at Ralph when Ralph accuses Jack of not wanting to be rescued. Ralph decides to join the hunters on their expedition to find the beast, despite his wish to rekindle the fire on the mountain. When they reach the other side of the island, Jack expresses his wish to build a fort near the sea.
The hunters, while searching for the beast, find a boar that attacks Jack, but Jack stabs it and it runs away. The hunters go into a frenzy, lapsing into their "kill the pig" chant once again. Ralph realizes that Piggy remains with the littluns back on the other side of the island, and Simon offers to go back and tell Piggy that the other boys will not be back that night. Ralph realizes that Jack hates him and confronts him about that fact. Jack mocks Ralph for not wanting to hunt, claiming that it stems from cowardice, but when the boys see what they believe to be the beast they run away.
Ralph returns to the shelters to find Piggy and tells him that they saw the beast, but Piggy remains skeptical. Ralph dismisses the hunters as boys with sticks, but Jack accuses him of calling his hunters cowards. Jack attempts to assert control over the other boys, calling for Ralph's removal as chief, but when Ralph retains the support of the other boys Jack runs away, crying. Piggy suggests that, if the beast prevents them from getting to the mountaintop, they should build a fire on the beach, and reassures them that they will survive if they behave with common sense. Simon leaves to sit in the open space that he found earlier. Jack claims that he will be the chief of the hunters and that they will go to the castle rock where they plan to build a fort and have a feast. The hunters kill a pig, and Jack smears the blood over Maurice's face. They then cut off the head and leave it on a stake as an offering for the beast. Jack brings several hunters back to the shelters, where he invites the other boys to join his tribe and offers them meat and the opportunity to hunt and have fun. All of the boys, except for Ralph and Piggy, join Jack.
Meanwhile, Simon finds the pig's head that the hunters had left. He dubs it The Lord of the Flies because of the insects that swarm around it. He believes that it speaks to him, telling him how foolish he is and that the other boys think he is insane. The pig's head claims that it is the beast, and it mocks the idea that the beast could be hunted and killed. Simon falls down and loses consciousness. After he regains consciousness and wanders around, he sees the dead pilot that the boys perceived to be the beast and realizes what it actually is. He rushes down the mountain to alert the other boys about what he has found.
Ralph and Piggy, who are playing at the lagoon alone, decide to find the other boys to make sure that nothing unfortunate happens while they are pretending to be hunters. When they find Jack, Ralph and Jack argue over who will be chief. When Piggy claims that he gets to speak because he has the conch, Jack tells him that the conch does not count on his side of the island. The boys panic when Ralph warns them that a storm is coming. As the storm begins, Simon rushes from the forest, telling about the dead body on the mountain. Under the impression that he is the beast, the boys descend on Simon and kill him.
Back on the other side of the island, Ralph and Piggy discuss Simon's death. They both took part in the murder, but they attempt to justify their behavior as motivated by fear and instinct. The only four boys who are not part of Jack's tribe are Ralph and Piggy and the twins, Sam and Eric, who help tend to the fire. At Castle Rock, Jack rules over the boys with the trappings of an idol. He has kept one boy tied up, and he instills fear in the other boys by warning them about the beast and the intruders. When Bill asks Jack how they will start a fire, Jack claims that they will steal the fire from the other boys. Meanwhile, Ralph, Piggy and the twins work on keeping the fire going but find that it is too difficult to do by themselves. They return to the shelters to sleep. During the night, the hunters attack the four boys, who fight them off but suffer considerable injuries. Piggy learns the purpose of the attack: they came to steal his glasses.
After the attack, the four boys decide to go to the castle rock to appeal to Jack as civilized people. They groom themselves to appear presentable and dress themselves in normal schoolboy clothes. When they reach Castle Rock, Ralph summons the other boys with the conch. Jack arrives from hunting and tells Ralph and Piggy to leave them alone. When Jack refuses to listen to Ralph's appeals to justice, Ralph calls the boys painted fools. Jack takes Sam and Eric as prisoners and orders them to be tied up. Piggy asks Jack and his hunters whether it is better to be a pack of painted Indians or sensible like Ralph, but Roger tips a rock over on Piggy, causing him to fall down the mountain to the beach. The impact kills him and, to the delight of Jack, shatters the conch shell. Jack declares himself chief and hurls his spear at Ralph, who runs away.
Ralph hides near Castle Rock, where he can see the other boys, whom he no longer recognizes as civilized English boys but as savages. He crawls to the entrance of Jack's camp, where Sam and Eric are now stationed as guards, and they give him some meat and urge him to leave. While Ralph hides, he realizes that the other boys are rolling rocks down the mountain. Ralph evades the other boys who are hunting for him, then realizes that they are setting the forest on fire in order to smoke him out-and thus will destroy whatever fruit is left on the island.
Running for his life, Ralph finally collapses on the beach, where a naval officer has arrived with his ship. He thinks that the boys have only been playing games, and he scolds them for not behaving in a more organized and responsible manner as is the British custom. As the boys prepare to leave the island for home, Ralph weeps for the death of Piggy and for the end of the boys' innocence.