The novel is set in an unspecified time, during an unnamed war. A British plane with schoolboys aboard is shot down as it flies over the Pacific Ocean. The accident results in several fatalities, including the pilot and all other adults. Luckily, the boys survive the ghastly crash. Their joy is short-lived, however, because they find themselves trapped on a deserted island. Ralph, the story’s protagonist, and Piggy, his sidekick, are the first two boys who meet ashore after the crash. Ralph is tall, confident, calm, and one of the older boys in the group. Piggy, on the other hand, is overweight, vulnerable, asthmatic, and wears glasses to correct his poor vision. However, unlike Ralph and the other boys, Piggy is remarkably intelligent and thoughtful. Not long after Ralph and Piggy meet, Ralph discovers a conch shell that he uses to assemble other survivors. He blows the shell, and the other boys come to the gathering. One of the most noticeable boys who emerges from the thickets is Jack Merridew. He is the aggressive, domineering leader of a marching choir.

Since Ralph took the initiative to blow the conch and bring the boys together, they decide he should be their leader on the island. Everyone except Jack supports this decision. Ralph, Jack, and another boy named Simon explore the island to examine its size and contents. During this expedition, they learn they are alone on the island and decide to adopt basic survival strategies to live until getting rescued. As they think about how to find food, they come across a wild pig, which they decide to eat. However, as Jack prepares to stab the pig, it escapes unharmed.

When the boys return from their expedition, Ralph convenes a meeting with all the boys to establish rules of order while on the island. Jack is one of the first boys to support Ralph's idea, but he does so only because he believes the existence of rules means that those who go against them will be punished. The intelligent Piggy is not happy with Jack's line of reasoning and questions his lack of concern regarding the most important issues that need to be solved, such as the boys’ long-term survival. Ralph believes that if the boys wish to ever escape the island, they must follow innovative survival strategies. He suggests that the boys create a fire on the mountain as a signal of their presence on the island to any vessels passing nearby. They agree with Ralph’s idea and start the fire, using Piggy’s glasses to light it. However, after some time, most boys give up on the fire after finding it difficult to maintain. Piggy argues that they should have focused on building shelters first before starting the fire since the smallest boys need a home on the island so they don’t get lost. Piggy worries that some boys might already be missing because they haven’t yet taken an accurate headcount of everyone.

The boys then divide into two groups: one to hunt for food, and the other to build shelter. Jack leads the hunting team while Ralph oversees the construction. However, the hunters decide to go swimming instead of doing their job, so Jack hunts by himself. Jack tells Ralph that he does not feel like he is hunting the wild pigs anymore; instead, he is being hunted. To make matters worse, the small boys do not provide substantial help with anything. Moreover, only Simon supplies consistent help in building shelters with Ralph. However, even Simon leaves his work behind to walk alone in the forest and explore nature. He finds a cool, open place in the jungle with beautiful bushes and fragrant flowers.

Eventually, the boys establish daily routines for themselves. The smallest and youngest boys are known as littluns, and their primary activity is to gather fruits. Notably, the littluns behave well and carry on with their gathering duties and play in a civilized manner, despite the absence of supervising adults. Hunting remains Jack’s area of expertise. Piggy contemplates constructing a sundial. Since the boys abandoned maintaining the signal fire, a ship passes the island without stopping to rescue them. The ship would have been the only hope for the boys to get rescued, but that hope fades as the ship moves further away from the island. As a result, Piggy becomes angry with Jack and blames him for ignoring the fire and focusing on hunting. Piggy’s words do not go over well with Jack, who believes that he has the sole discretion to choose his daily duties. So he punches Piggy in the face, breaking his glasses. When Jack and the hunters finally succeed in killing a wild pig, they celebrate by chanting and dancing demonically around its carcass. In their sinister dance, Simon acts like a pig, and the rest of the boys pretend to be the hunters attacking him. When their dance devolves into violence, a boy named Maurice sustains injuries as a result.

After realizing the boys’ emerging cruelty, Ralph acknowledges Piggy's maturity and worries about Jack’s increasingly savage behavior. He convenes an urgent meeting wherein he reprimands the boys for not being of any help in the construction of the shelters and the maintenance of the fire. According to him, their only hope for survival is keeping the fire alive, and it must be located on the mountain. Ralph feels fearful and isn’t sure why, yet he reassures the boys that there is no reason to be afraid. In contrast, Jack believes that the littluns are of no help on the island and yells at them, admonishing them for their feebleness and inability to do anything well. When the littluns express fear of a beast on the island, Jack refutes them. However, one of the boys discusses a nightmare he had, after which he awoke to see something moving in the trees. Simon responds that the figure in the trees was likely him because he had been walking around the jungle that night. Nevertheless, the lilluns remain unconvinced and still believe the beast exists. Some think the beast is a ghost, whereas others are sure it is a squid.

Another conflict arises between Piggy and Ralph. Their dispute makes clear the boys’ collective descent into savagery. Jack reinforces this notion by believing that no one cares about the rules that had been set during the second meeting. Ralph says that if the group decides to abandon the rules, nothing will hold them together, and their plans to survive and get rescued will fail. Jack does not believe that Ralph's words make sense anymore, so he abandons the group with most of the other boys. He leads them on an expedition to capture the beast, but Jack’s other goal is to forge his own kingdom with them as his subjects. Only Piggy, Simon, and Ralph are left behind. Piggy knows of Jack’s intentions to take control of the group and warns Ralph that if this comes to pass, the boys will die on the island.

That night, an aerial battle in the ongoing war occurs, and one pilot falls out of a military plane and dies after landing in the trees. The next morning, twin boys named Sam and Eric — known to the others as “Samneric” — discover the dead pilot as they rekindle the fire on the mountain. Without inspecting the body, they believe it is the beast and rush down the mountain to the shelters to wake the other boys. Piggy argues that the boys should remain in their shelters, believing the beast won’t approach them there. However, Jack persuades his followers to plan a hunt for the beast. Ralph reluctantly agrees to go with Jack to pursue the beast, although he would prefer to manage the fire. As the boys traverse the island looking for the beast, they reach the its other shore, and Jack expresses interest in building a fort there.

One wild boar attacks Jack as he and the other hunters enter the deep thickets of the forest. He stabs it with his spear, and it flees. The hunters start dancing and chanting in the same sinister way they did just before Maurice was injured. During the hunt, Ralph realizes that Piggy was not part of the group and chose instead to remain with the littluns at the shelters. As sunset nears, Simon offers to return to the shelters to inform Piggy and the littluns that the hunters will not return until the following day. As Simon leaves, it becomes clear to Ralph that Jack harbors hatred toward him, so he decides to talk to him about it. Jack does not hesitate to tell Ralph that he is a coward who had not initially committed himself to hunting for the beast. During their confrontation, the other boys run away after seeing what they think is the beast.

When Ralph gets back to the littluns, he finds Piggy and informs him that they saw the beast in the forest. Piggy does not believe this to be true, but he restrains himself from saying more about the matter. Ralph, still simmering in his tension with Jack, says that hunters are merely boys with sticks. Jack does not take these words lightly. He believes that Ralph has belittled him and that he has called the hunters cowards. In retaliation, Jack tries to convince the boys to abandon Ralph and elect him as their leader, but do not support his bid. After the botched attempt to replace Ralph, Jack flees from the group in tears.

In response to rising fears about the presence of the beast on the mountain, Piggy suggests the boys move their signal fire to the beach. He argues that if the boys embrace a sense of maturity and civilization, they will survive their predicament and return home. Simon then leaves the group for his usual spot where he goes to watch the flowers and bushes. At the same time, Jack proclaims himself the leader of the hunters and decides to lead them to Castle Rock, an elevated cliff near another edge of the island. The hunters pledge their support to him. Jack's hunters kill a wild pig and organize a celebratory feast. They cut off its head and decide to give it to the beast as a peace offering. After leaving the pig’s head on a stake for the beast, Jack feeds the boys and encourages them to be free and have fun. Everyone joins the feast except Ralph and Piggy.

As he wanders around the island alone, Simon discovers the pig’s head and decides it is the Lord of the Flies because flies surround its decaying, bloody head. Simon then hallucinates the Lord of the Flies speaking to him. The Lord of the Flies admonishes Simon and tells him the other boys will think he has a mental problem. The Lord of the Flies also claims it is the beast. Upon hearing this, Simon faints. Some moments later, he regains consciousness and continues his walk around the island. He comes across the body of the pilot that the hunters had thought was the beast. He takes his time to study it and understands it is, in fact, not the beast. Simon then decides to go back down the mountain to explain to the boys that the “beast” is a dead pilot.

Near Castle Rock, Jack and Ralph argue again about who should be the chief of the boys. Piggy tries to intervene, claiming he should be granted the opportunity to settle their conflict since he has the conch. However, on Jack’s side of the island, the conch commands no authority. Just before a storm hits the island, Simon emerges from the thickets. Thinking that Simon himself is the beast, the boys pounce. Violence ensues, and Simon dies.

Piggy and Ralph feel remorseful about Simon's death, especially because they participated in his murder. They justify their actions by telling each other they behaved out of fear and never intended to kill Simon. At this point, almost every other boy on the island has fled from Ralph’s camp to join Jack on Castle Rock. Only Piggy and Samneric remain loyal to Ralph. The twins continue to tend to the fire. On the other side of the island, Jack has taken over, instilling fear in the boys by threatening them. He manipulates the boys by warning them of the beast he doesn’t believe exists. He even keeps one boy tied up to scare the others. Back at Ralph’s camp, Piggy, Samneric, and Ralph try as hard as they can to keep the fire alive, but their efforts do not yield substantial results. They give up and return to the shelters to rest. In the middle of the night, Jack’s hunters wake them up, and the boys fight. Ralph, Piggy, and Samneric are outnumbered and overwhelmed. The hunters steal Piggy’s glasses.

Ralph’s few followers plan to go and face Jack to resolve their differences in a civilized manner. They make the necessary preparations to be presentable when they appear before the hunters. Upon reaching Castle Rock, Ralph blows the conch to assemble the boys. When Jack comes to the vicinity from the bushes, he informs Ralph that the boys are comfortable and should not be disturbed. This angers Ralph, who calls the boys “painted fools.” Jack’s cronies capture and tie up Samneric. When Piggy criticizes the boys’ behavior, another boy named Roger angrily hits him with a rock, causing Piggy to topple from the edge of Castle Rock. He falls over the cliff and onto the wet, jagged rocks below. Piggy dies instantly, and the conch — previously a symbol of order and unity — shatters beyond repair. Jack’s next target is Ralph, who flees just as a spear flies at him.

Ralph finds a hiding place somewhere near Castle Rock. After some time, he creeps back to the camp and finds that Samneric have become its guards. They offer some food to Ralph and beg him to leave. The other boys start throwing rocks down the hill to scare Ralph away. When they realize that this strategy may not be successful, they start a forest fire to force him out. He runs for his life and finally finds himself back at the beach. He collapses. Then a naval officer arrives on the island in response to the fire. He believes the boys have been playing silly games and rebukes them for not behaving in a civilized manner. The surviving boys are rescued.