Todd lives in the remote settlement of Prentisstown on a planet called the New World. He grows up believing that a race of aliens called the Spackle released a “Noise germ” that infected and killed all the women in his settlement, while giving men the ability to hear others’ thoughts. Just when Todd is one month away from becoming a man in his settlement, he goes out walking with his dog Manchee in the nearby swamp and comes across a “hole” in the Noise. He fears that this means the Spackle are coming back to fight again.
But when Todd’s own Noise reveals the Noise hole to the other residents of Prentisstown, including the leader Mayor Prentiss and a fiery local preacher named Aaron, Todd’s adoptive parents Ben and Cillian tell Todd that he has to get out of the settlement immediately. They reveal that they have been secretly preparing for him to leave for a while and even already have a bag packed. Ben gives Todd a knife for his journey as well as Todd’s Ma’s journal, which contains a map and a note from Ben.
Todd is reluctant to leave, but when the local sheriff Mr. Prentiss Jr. (son of Mayor Prentiss) comes to Ben and Cillian’s house, a fight breaks out, and soon more men are out chasing after Todd. At last, Todd agrees to go off with Manchee and follow the river to the next settlement, leaving Ben and Cillian behind.
Todd follows the river back to the swamp and soon learns that the hole in the Noise he heard was actually a girl about his age named Viola. Todd is surprised, since he didn’t think any girls or women were still alive on the planet, and Viola remains cautious by staying silent around Todd for a while after they first meet. Eventually, Viola speaks up, and Todd learns that she was part of a scouting ship that came from a larger settlement ship on its way to the New World. Viola’s parents died when the ship crash-landed, leaving Viola as the only survivor.
At one point, the zealous preacher Aaron attacks Todd and Viola. Aaron seems ready to kill Todd, and although Todd eventually gets a chance to kill Aaron, he chooses not to use his knife after all. Todd and Viola soon learn that it’s not just Aaron following them: a whole army is coming from Prentisstown.
Todd and Viola eventually manage to evade the army by destroying a bridge behind them. They make it to their first destination of Farbranch, where a local woman named Hildy offers them hospitality, although other residents of the settlement view Todd with suspicion because he comes from Prentisstown. To the surprise of the people in Farbranch, the Prentisstown army finds another bridge and comes across to attack their town. In the confusion, Todd and Viola escape.
Todd and Viola embark on a journey to reach Haven, which is supposedly the biggest settlement in the New World. Todd believes it is the only settlement with enough people to resist the Prentisstown army, and Viola believes it may have the technology to allow her to communicate with her settlement ship (which is still seven months away from arriving) and warn them about conditions on the planet, such as the Prentisstown army.
For the early part of the journey, Todd often regrets not being able to work up the courage to use his knife to kill. But when he finally gives in to this urge and kills a Spackle, he realizes with horror afterwards that the Spackle was probably innocent. Todd also learns from Viola that much of what he grew up hearing in Prentisstown was a lie—the Spackle are peaceful, and Mayor Prentiss only waged war on them to distract from the settlement’s other problems.
Aaron catches up with Todd and Viola, attacking them again. He manages to kidnap Viola and wound Todd with Todd’s own knife. Todd chases after Viola and starts to hallucinate, seemingly due to the fact that Spackle blood got into his bloodstream when Aaron stabbed him. Todd succeeds in rescuing Viola before Aaron can sacrifice her in a ritual, but Aaron manages to catch and kill Manchee.
Soon after, Todd passes out, and Viola manages to take Todd to the nearest settlement. There, a man named Doctor Snow treats Todd’s disease. Todd recovers just in time to speak with Ben, who managed to escape Prentisstown. When the Prentisstown army reaches this new settlement, Todd, Ben, and Viola flee again for Haven.
On the last part of their trip to Haven, Ben explains to Todd the truth about Prentisstown: the women didn’t die of a disease. Instead, the men of the town killed the women at Mayor Prentiss and Aaron’s command, including Todd’s Ma and the former mayor, Elizabeth. Ben then leaves Todd and Viola, as he knows people don’t trust men from Prentisstown and he doesn’t want to be a liability to Todd.
Viola finally reads Todd his Ma’s journal (since Todd himself is illiterate). Todd is moved to hear about how hopeful his Ma was in the early days of the settlement, but he can’t bear to hear her final words quite yet.
During the final day of Todd and Viola’s trip to Haven, Aaron once again attacks. Aaron’s goal seems to be to provoke Todd into attacking him, in order to turn Todd into a killer. Todd wrestles with the question of whether he should kill Aaron to protect himself and Viola, but ultimately Viola is the one who kills Aaron with Todd’s knife. Shortly afterwards, Mr. Prentiss Jr. surprises them and manages to shoot Viola.
Todd runs with a seriously injured Viola toward Haven, just barely managing to avoid Mr. Prentiss Jr. Todd thinks that they have escaped to safety, only to find Mayor Prentiss himself waiting for them in Haven. Mayor Prentiss reveals that he rode ahead and got Haven to surrender just by threatening them with the size of his army. Todd realizes that he can’t hear the mayor’s Noise for some reason. Mayor Prentiss introduces himself as the president of the New World and welcomes Todd to the new capital city.
