Lord of the Flies is set on a tropical island in the Pacific Ocean, shortly after some form of nuclear holocaust in Europe. A group of boys survive a plane crash and are left stranded on a deserted island with no adults. They form a unique societal microcosm where they have free rein to do as they please.

The boys do try to establish rules and discipline on the island, and they vote democratically to elect Ralph as their leader. Ralph attempts to maintain order in the group, but he has a rival and antagonist in Jack, leader of a set of choir boys. Ralph decides to give Jack and the choir boys the role of hunters, which puts him in good standing with Jack.

Ralph is supported by a nerdy boy nicknamed Piggy. He is mature and rational, but because he is fat and wears thick glasses he is constantly ridiculed by the other boys. Ralph becomes Piggy's only friend, as well as his protector from the other boys' relentless bullying. Piggy's glasses become very significant, as they are used to light the first fire on  the island. The hunters are then given the responsibility of keeping the fire going as a signal fire, in the hope that a passing ship might rescue them.

Ralph finds a conch on beach, and it comes to represent his authority on the island. Whenever the conch is blown, the boys come together; only the boy holding the conch can speak.

As time passes, their civilised order starts to break down. The boys become lazy and primitive. Jack and the hunters become obsessed with hunting pigs and lose sight of Ralph's democratic vision. Stories of a beast supposedly hidden deep in the jungle emerge, and the boys start to venerate this unseen creature.

One day, Ralph notices a ship in the distance, but he realises the signal fire is not lit, as Jack and the hunters have neglected their duties. Ralph frantically races up the mountain to light the fire, but the ship has passed. He angrily confronts Jack and the hunters, and the sense of division grows between the boys.

Jack and the hunters begin to take on a more primitive, tribal appearance, painting their faces and performing wild dances and chants. Their violent behaviour worsens, and their characters become demonic.

A fighter plane is shot down over the island, and a dead pilot floats down on a parachute and gets stuck in a tree. The boys decide he must be the beast in the jungle and they become paranoid with fear.

Jack rebels against Ralph's authority and tries to assume the role of chief. When he fails in his leadership challenge, he leaves the tribe along with the older boys. He and the hunters kill a wild pig and stick its head on a pole as a sacrifice to the beast. They have become wild with hatred and lust, and this is reflected in the bloody, smiling face of the pig.

Simon, a good and pure boy, spots the pig's head. In his fear and shock at the hideous sight, he has a hallucination: he hears the pig speaking to him. This leads him to the realization that there is no beast on the island. The real beast is the evil that exists within the boys. Simon also recognizes the dead parachutist for what he is.

Simon races back to the boys to reveal the truth, but they are busy feasting on a pig and taking part in a frantic tribal dance. Mistaking Simon for the beast, they brutally beat him to death.

Jack's hunters have stolen Piggy's glasses, without which he cannot see. Ralph and Piggy go to Jack's tribe to try to retrieve the glasses. Ralph attempts to use the conch, but to no avail, as the hunters refuse to acknowledge his authority. Instead, Piggy is killed and the conch is shattered to pieces.

Ralph flees. Jack and the hunters pursue him. In an attempt to trap Ralph, Jack accidentally sets fire to the entire island. Ralph staggers onto the beach and finds himself face-to-face with a British Naval officer. The devastating fire has brought about the boys' rescue.