In the midst of a wartime evacuation, a British plane crashes on or near an isolated island in a remote region of the Pacific Ocean. The only survivors are boys in their middle childhood or preadolescence. Two boys—the fair-haired Ralph and an overweight, bespectacled boy nicknamed "Piggy"—find a conch, which Ralph uses as a horn to call all the survivors to one area. Due largely to the fact that Ralph appears responsible for bringing all the survivors together, he is quickly elected their "chief", though he does not receive the votes of the members of a boys' choir, led by the red-headed Jack Merridew. Ralph asserts three primary goals: to have fun, survive, and to maintain a smoke signal that could alert passing ships to their presence on the island. The boys declare that whoever holds the conch shall also be able to speak at their formal gatherings and receive the attentive silence of the larger group.
Jack organises his choir group into a hunting party responsible for discovering a food source. Ralph, Jack, and a quiet, dreamy boy named Simon soon form a loose triumvirate of leaders. Though he is Ralph's only confidant, Piggy is quickly made into an outcast by his fellow "biguns" (older boys) and becomes an unwilling source of laughs for the other children. Simon, in addition to supervising the project of constructing shelters, feels an instinctive need to protect the "littluns" (younger boys).
The semblance of order quickly deteriorates as the majority of the boys turn idle, giving little aid in building shelters, and begin to develop paranoias about the island, referring to a supposed monster, the "beast", which they believe to exist on the island. Ralph insists that no such beast exists, but Jack, who has started a power struggle with Ralph, gains control of the discussion by boldly promising to kill the beast. At one point, Jack summons all of his hunters to hunt down a wild pig, drawing away those assigned to maintain the signal fire. A ship travels by the island, but without the boys' smoke signal to alert the ship's crew, the ship continues by without stopping. Angered by the failure of the boys to attract potential rescuers, Ralph considers relinquishing his position, but is convinced not to do so by Piggy.
One night, an aerial battle occurs over the island while the boys sleep, during which a dead fighter pilot is ejected from his plane. His body drifts down to the island in his parachute; both get tangled in a tree near the top of the mountain. Later on, while Jack schemes against Ralph, twins Sam and Eric, now assigned to the maintenance of the signal fire, see the corpse of the fighter pilot and his parachute in the dark. Mistaking the corpse for the beast, they run to the cluster of shelters that Ralph and Simon have erected and warn the others. This unexpected meeting again raises tensions between Jack and Ralph. Shortly thereafter, Jack decides to lead a party to the other side of the island, where a mountain of stones, later called Castle Rock, forms a place where he claims the beast resides. Only Ralph and Jack's sadistic supporter Roger agree to go; Ralph turns back shortly before the other two boys. When they arrive at the shelters, Jack calls an assembly and tries to turn the others against Ralph, asking for them to remove him from his position. Receiving little support, Jack, Roger, and another boy leave the shelters to form their own tribe. This tribe lures in recruits from the main group by providing a feast of cooked pig and its members begin to paint their faces and enact bizarre rituals including sacrifices to the beast.
Simon, likely an epileptic, wanders off on his own to think and finds a severed pig head, left by Jack as an offering to the beast. Simon envisions the pig head, now swarming with scavenging flies, as the "Lord of the Flies" and believes that it is talking to him. The pig's head tells Simon that the boys themselves "created" the beast and claims that the real beast is inside them all. Simon also locates the dead parachutist who had been mistaken for the beast, and is the sole member of the group to recognize that the "monster" is merely a human corpse. Simon, hoping to tell others of the discovery, finds Jack's tribe in the island's interior during a ritual dance and, mistaken for the beast, is killed by the frenzied boys. Ralph, Piggy, Sam, and Eric feel guilty that they, too, participated in this murderous "dance."
Jack and his band of "savages" decide that they should possess Piggy's glasses, the only means of starting a fire on the island, so they raid Ralph's camp, confiscate the glasses, and return to their abode on Castle Rock. Ralph, now deserted by most of his supporters, journeys to Castle Rock to confront Jack and secure the glasses. Taking the conch and accompanied only by Piggy, Sam, and Eric, Ralph finds the tribe and demands that they return the valuable object. Turning against Ralph, the tribe takes Sam and Eric captive while Roger drops a boulder from his vantage point above, killing Piggy and shattering the conch. Ralph manages to escape, but Sam and Eric are tortured until they agree to join Jack's tribe.
The following morning, Jack orders his tribe to begin a manhunt for Ralph. Jack's savages set fire to the forest while Ralph desperately weighs his options for survival. Following a long chase, most of the island is consumed in flames. With the hunters closely behind him Ralph trips and falls. He looks up at a uniformed adult - a naval officer whose party has landed from a passing warship to investigate the fire. Ralph bursts into tears over the death of Piggy and the "end of innocence". Infected by his emotion, Jack and the other children, filthy and unkempt but suddenly reverting to their true ages, also spontaneously erupt into sobs. After expressing disappointment that "British boys" had fallen into such feral behaviour, the officer awkwardly turns away to give them a moment to pull themselves together.