Lord of the Flies is the story of a group of boys whose plane crashes during the wartime evacuation of English schoolchildren. All adults are killed in the crash, and despite early attempts at organization, spearheaded by a boy named Ralph, the boys quickly descend into inhuman behavior that begins with the taunting of an overweight boy known as Piggy and ends with the formation of a savage, bloody society. When the boys are rescued they are confronted with the horrors of their own actions.
The novel opens with a fair-haired, physically fit boy named Ralph, walking through a jungle, leaving the wreckage of a plane that has crashed into the island. He soon meets another boy, who is overweight, has asthma and wears glasses. He tells Ralph about himself, the aunt he lives with, and that at school the other boys call him "Piggy." They find a large platform made of pink granite and in the lagoon formed by a large barrier reef that skirts the island, they discover a large conch shell. Piggy, who has seen one before, instructs Ralph how to use it, and with the resonant sounds from the conch shell, Ralph calls together any other boys who might be on the island.
Boys gather on the platform, and Piggy takes their names as they sit and wait for Ralph to speak. An organized group of boys arrives, marching in formation. Their leader informs the others that they are a choir, and he is in charge of them. His name is Jack Merridrew, and he immediately insults Piggy. Ralph suggests that they elect a chief, and though Jack wishes to be placed in the position, Ralph is elected. Jack is still allowed to be in charge of his choir, which are designated as "Hunters." Ralph decides to form a party to explore the area. Ralph selects Jack and one of the choir boys, Simon, to accompany him.
The three boys decide to climb a nearby mountain to get a view of the entire island. In the jungle they find tracks made by animals and a large boulder, which they roll down the side of the mountain. At the top they find that the island is uninhabited. They return to the beach, and Ralph blows the conch to call an assembly. One of the small boys, or "littluns" as they come to be called, asks about a "beastie" which he saw. The littluns are frightened, but the bigger boys assure them that there is no beast.
Ralph decides that they should make a fire at the top of the mountain, using the smoke as a signal to any ships that might pass by. The boys excitedly head to the top of the mountain, where they light a giant fire, using Piggy's glasses. Jack and his Hunters volunteer to take turns keeping the fire lit, so a steady signal can be maintained. The fire quickly spreads, setting other parts of the forest alight. Piggy criticizes the group's disorganization, and expresses the need for order, especially to know how many boys are on the island, so that they can keep track of everyone. The boys sneer at the idea, but Piggy points out that already the boy who complained about the beast is missing. This frightens the boys, and Ralph begins to understand the significance of their situation.
Time passes, and Jack develops into a real hunter, becoming ever more focused on successfully killing a pig. Ralph remains interested in keeping the fire lit as well as building shelters for protection during the night and rainstorms. He is frustrated at the lack of help he gets from the other boys. Only Simon can be counted on to help, but he also occasionally sneaks off to a secret spot in the jungle that he has discovered. One day, Jack comes back from an unsuccessful hunt, and Ralph confronts him about his lack of support. He also informs him of increasing talk amongst the littluns about a beast, and the growing fear that they are feeling. During their conversation, Jack and Ralph realize that their friendship is fracturing.
Repeatedly unsuccessful when hunting, Jack hatches a plan to paint his face with clay, so as to disguise himself from the pigs. He gathers all his hunters to him, including those who are meant to tend the fire. During this hunt, Ralph sees a ship on the horizon, and discovers that the fire on the mountain has gone out. The hunt returns, successful, and at the top of the mountain Ralph confronts Jack about the failure to maintain the fire. He informs the group that a ship passed by and that they missed the chance to be rescued. Under pressure, Jack apologizes, but remains excited at his success as a hunter. They rebuild the fire and Jack's excitement spreads to all the boys, as they all take part in the feast of meat that is a result of the hunt. Ralph becomes angry and leaves.
Ralph calls an assembly, where he confronts the boys about the need to maintain order, and above all, to keep the fire lit. The subject of the beast is brought up, and the littluns remained scared. Piggy vehemently denies its existence, as does Jack. Simon attempts to suggest that it is within everyone, but his inarticulateness is ridiculed. In their fear, the boys become overexcited and Piggy attempts to ground everyone in facts and reason, leading Jack to insult him. Ralph tries to make him allow Piggy to speak and the meeting breaks up when Jack refuses to follow the rules. He leaves the platform in a flurry of shouts and excitement and the boys soon follow him. Ralph, Piggy and Simon are left to consider the ruins of the assembly.
The twins, Sam and Eric, see something at the top of the mountain that they think is the beast, and a party is formed to find it. They do not, but in a meeting after the expedition, Jack finally breaks off from the group and establishes himself at Castle Rock. He gets other boys to join him, and a new, more savage tribe with a focus on hunting is established. During the night they steal Piggy's glasses, so they can start fires of their own. The next day, Simon has a conversation with the Lord of the Flies in the forest. He discovers that the beast that everyone is afraid of is not an animal that can be hunted, but is indeed something within them all.
Ralph, Piggy, Sam and Eric approach Castle Rock in an attempt to retrieve the glasses. The group of boys under Jack begin their hunting chant and work themselves into a frenzy. Simon emerges from the forest at this time, intent on telling everyone what he learned from the Lord of the Flies. He ends up in the center of the circle formed by the chanting boys and is killed. Piggy is killed by a boulder pushed by Roger, and Sam and Eric are forced to join the tribe. Ralph is left alone, and he finds out that Jack intends to hunt him down and kill him. He hides in the forest but the tribe sets the jungle on fire in order to force Ralph out. Ralph runs out of the jungle, towards the beach near the platform. There he is greeted by a Naval officer, who saw the smoke from the fire and came ashore to investigate. Ralph informs him that two boys have been killed, and in the face of rescue, Ralph breaks down and begins to weep for Piggy and the others.