Thirteen-year-old Todd Ness is the last boy in Prentisstown, an outpost of settlers on a planet other than Earth. Settled 10 years before Todd was born, most of the other settlers on the planet were killed by Spackles, indigenous creatures to the planet.
When he turns 14 in a month, he will be considered a man. All of his friends have already “become men,” so they can no longer play with him. For some time now, Manchee, his dog, has been his only companion. It is not so bad as Todd is able to hear Manchee’s thoughts, just as he can hear every other animal’s and man’s thoughts. The same virus that cursed men with this ability also killed all the women in Prentisstown. Todd has been raised by Ben and Cillian, two men who knew his parents well.
Sent by Ben to gather apples in the swamp outside of town, Todd and Manchee discover a place of silence, a phenomenon neither has experienced before. Even the swamp creatures are thinking simple thoughts of food and fear. Manchee tries to find the quiet, but is not able to track it before it moves away.
Todd tries to keep his discovery a secret, but it is impossible. His foster parents are able to hear his thoughts. They insist that Todd must leave Prentisstown. It is something they had planned for a while, and so his backpack is filled with supplies.
Ben leads Todd and Manchee to the river, as Cillian creates a diversion at their farm. As they flee, Ben tells Todd that much of what he has been told in his life is a lie. There are other settlements on the planet that survived.
Ben has provided him with a map and a journal written by Todd’s mother. They hear gunshots. They know that Mayor Prentiss and his men are at their farm and that Cillian has probably been shot. Ben leaves Todd by the swamp and runs back to help Cillian.
As Todd and Manchee run along the swamp, they come face to face with Aaron, the crazy preacher who has already hit Todd once that day. Todd knows that Aaron sent the men from town after him because he heard the quiet. While Aaron strangles Todd, a crocodile attacks the man. Todd escapes and runs right into the quiet, which turns out to be a girl about his age.
Aaron comes through the brush and tries to strangle Todd again, but this time Manchee attacks him. Aaron escapes, but he takes the girl with him. Todd follows, and they fight again. Aaron tries to drown the boy, but Todd repeatedly hits the man’s head with a rock.
When Aaron passes out, Todd knows he should take the knife from his pack and kill him, but he can’t do it. He, Manchee and the girl run away together. She leads Todd to the spaceship that carried her and her parents to the planet. It crash-landed, and her parents were killed. She retrieves a pack of supplies from the craft, and they continue on. When they stop for the night, Todd realizes that she must not have caught the Noise disease that killed all the women. As he thinks this, he realizes she can hear his thoughts. He tries to convince her that she may still survive, but she becomes distraught.
The following morning, they wake to find Mayor Prentiss and a posse close behind them. They cross a wooden bridge over a ravine, and then the girl uses something from her pack to blow it up so their pursuers can’t cross. The girl finally speaks and tells Todd her name is Viola.
Soon they meet Mathilde, an old woman with a rifle, who is not happy they blew up her bridge. Todd is shocked to find another woman alive since he has been taught that all the women died from the Noise disease. Mathilde takes them to her house to meet her husband, Tam. They feed the children and give them a place to stay for the night before taking them to Farbranch, the nearest town.
The people there are hostile to Todd when they hear from his noise that he is from Prentisstown, but Todd does not understand why. Before they can vote whether to allow Todd to stay, an army from Prentisstown attacks them. It seems that every man from Prentisstown now rides with the mayor. Their sole goal is to find Todd. He, Viola and Manchee flee again. The town is on fire behind them.
Davy Prentiss, the mayor’s son, finds them the following day. Todd learns that the men do not want Viola. They are only searching for him. Todd and Davy fight, with Todd eventually pulling his knife on the mayor’s son, but once again, he is not able to kill his attacker. Viola stops Todd from being killed when she tazes Davy with a device from her ship. They leave him tied up and search for a place called Haven, which is supposedly the biggest settlement of people left on the planet.
Todd sees a Spackle near a river, and he has been taught that these creatures are his enemy. He chases the creature down. He is shocked to hear how afraid the creature is of him and how weak it is. Todd kills it anyway and then suffers from guilt as he realizes the creature would never have hurt him.
Like a bad nightmare, Aaron finds them again, stabs Todd and takes Viola. Todd survives, and he and Manchee devise a plan to save Viola. Tragically, Aaron captures the dog as Viola and Todd make their escape. He screams for Todd to return or he will kill the dog. Todd must watch helplessly as Aaron breaks Manchee’s neck.
Todd’s wound becomes infected. Viola finds another town with a doctor who can help him, but the men in the town refuse to listen to Viola about the coming army from Prentisstown. The women are kept outside this town in a dormitory. They are allowed to cook, clean and procreate with the men, but they are not allowed to live with them.
The men keep music playing over loudspeakers to hide their thoughts from the women. In spite of the noise, Todd hears a song that Ben used to sing to him as a child. He follows the sound and finds his foster father.
Todd learns that the mayor’s men killed Cillian. He tells Ben everything that happened to him. The men from the town find them and are convinced they are spies for the coming army. Ben keeps urging them to search Todd’s noise to prove that he does not know anything about the army or about the law. Todd hears that the law demands that any man who leaves Prentisstown be killed.
Ben, Todd and Viola escape. When they stop to rest, Ben finally explains what happened in the past. The Noise germ was something that happened naturally, as soon as the settlers left their spacecraft. The Spackle had nothing to do with it. The constant Noise, however, drove some of the men crazy, and that is when they started the war with the Spackle.
When the Spackle fled, the men were left with the Noise. Some, especially those in Prentisstown, began to despise the fact that the women were silent. Aaron and Prentiss began to spread lies that the women were evil and had to be destroyed. Although Ben and Cillian did not agree, they did not fight the others because Todd’s parents had begged them to keep their son alive.
A few women escaped to tell the other settlers what had happened. It was then that the men of Prentisstown were exiled to their small piece of land. Any men who left the area had to be killed so they would not spread their hatred further. When Davy Prentiss finds them again, Ben sacrifices his life so Todd and Viola can escape.
Before Todd and Viola reach Haven, Aaron attacks them again. Todd finally realizes that it is a rite of passage in the town. All boys must kill someone in order to become men. That way, no man in Prentisstown can ever claim he has no blood on his hands.
Aaron demands Todd kill him to fulfill his destiny, but Todd refuses. Aaron attacks Viola, to spur Todd’s anger. He and Todd fight, but still when Todd has an opportunity to plunge his knife into Aaron, he doesn’t do it. Viola is the one who eventually stabs Aaron, but the man continues live. Beaten to a bloody pulp and stabbed several times, he stumbles over the edge of a waterfall to his death.
Shaken and exhausted, Viola and Todd walk the final miles to Haven but are stopped by Davy Prentiss. He shoots Viola. Todd fights him and then carries Viola to the town, only to discover Mayor Prentiss and the men from Prentisstown have already captured it.
Todd can no longer hear the mayor’s thoughts. Prentiss informs him that he is now President Prentiss of New Prentisstown. Todd recognizes they have run right into a trap, and the only thing he can do is beg for Prentiss to save Viola.