There's a boy named Todd who lives in this weird place called Prentisstown with his dog, Manchee. What's so weird about Prentisstown? Well, there are no women in Prentisstown, for starters, and there's also this weird germ called Noise that makes everyone's thoughts loud enough for everyone else to hear. So yeah, weird place.
One day, Todd is taking a stroll through the swamp nearby (since he's the youngest person in Prentisstown, he gets stuck with boring jobs, like picking apples), when out of the blue, he hears a hole in the Noise, a.k.a. silence. Whoa. After this silence disappears, Todd has an ugly run-in with the ill-tempered preacher from church, a dude by the name of Aaron.
Todd goes back to Prentisstown and his foster parents, Ben and Cillian. These guys have been taking care of him since he was a baby, when Todd's parents were killed in a great war (where these aliens called Spackle tried to take over the world). Ben and Cillian hear about the hole in Todd's Noise and tell him that he has to leave town. Like, right now and forever. Yikes.
While the mayor's son is banging on the front door, Todd runs back toward the swamp. And guess what? He runs into Aaron again—and even stranger, he seems to be chasing Todd. Crocodiles get involved and Todd and Manchee manage to slip away, leaving Aaron to the crocs.
Todd stumbles into the source of that silence he heard, and it's beyond anything he could have imagined: It's a girl (you may remember that Todd's never seen a girl in Prentisstown). Turns out she landed on a space ship coming from the Old World to the New World, but when her ship crashed, it left her the lone survivor.
Right away, there's a serious communication issue: Todd's also never been around someone who doesn't have Noise. It's as weird for him as the idea of Noise is to us. But they don't have too much time to resolve their differences because Aaron comes after them again, maimed by the croc-attack. After escaping the preacher yet again, Todd and Viola (that's the girl) set off together, heading away from Prentisstown.
One problem: They don't know where they're going. Looking for an answer, Todd opens up a book that Ben gave him before he left—it's a diary of his mom's. Unfortunately, though, he can't read it since they weren't allowed to be educated in Prentisstown.
In their adventures, Todd and Viola meet Hildy and Tam, a friendly couple who help them get to Farbranch. Mystery of mysteries, Tam and Hildy are happy together, even though the Noise germ is supposed to kill women. They take refuge in Farbranch, a nearby settlement, but unfortunately, the Prentisstown army shows up. Todd and Viola flee the town as the Mayor's army burns it to the ground. Their next stop is Haven—where they will find safety.
During their journey, they come across a Spackle—one of those alien creatures long thought to be extinct. Todd fights the Spackle to the death, though something seems to be wrong because the Spackle comes across as scared and harmless. After it's dead, Todd's totally overcome with guilt. Things get way worse, though, when Aaron shows up and carries Viola off. After stabbing Todd in the back.
Todd wakes up and has one thought: He has to find Viola. Battling a raging fever, he straggles across the land until he finds Aaron, and after a fever induced battle with himself in third person (strange, yes) he decides that he has to try to rescue Viola, killing Aaron if need be.
Using Manchee as bait, he manages to lure Aaron away and get Viola back. Sadly, Manchee's life is sacrificed in the process. Todd and Viola sail down river until they are rescued by a man named Doctor Snow; Todd wakes up in a hospital bed days later.
Doctor Snow is nice enough, but something seems afoot. Plus, the people in his settlement don't seem to realize that this army is on its way, destroying one settlement at a time. On a walk outside of town, Todd is reunited with his foster-father, Ben. Snow and his men catch up with them, though, and threaten to kill them both. Why? Apparently, every man from Prentisstown is an outlaw in the rest of the world. And yeah, we don't think that's much of an explanation either, but it's all we've got right now
Doctor Snow lets them go in the end, and Ben urges Viola and Todd to run ahead to Haven. He also reveals the secret that's has been haunting Todd all along: Prentisstown wasn't actually at war with the Spackle, and the Noise germ didn't kill the women. The men of Prentisstown killed both the Spackle and the women. Yep, that's why Todd's hometown has such a bad reputation. Bummer.
Todd and Viola finally see Haven in the distance. But there are two things in the way. The first is Prentiss Jr., the mayor's son, but they manage to get past him without too much trouble. The second thing in their way, however, is Aaron.
They take refuge in a stone church, which is built under a huge waterfall leading to Haven. Aaron finds them (it's kind of his thing) and Todd is finally faced with a decision he's been battling all along: whether or not to kill. Aaron and Todd wrestle until Viola does what Todd won't do, and uses the knife to kill Aaron. Aaron, in his last moments, falls off the waterfall.
After the debacle in the church, they run into Prentiss Jr. They manage to run from him, but not before he shoots Viola in the stomach. Todd carries Viola the rest of the way.
And here's the grand finale. After this fiasco, they get to Haven. And it's completely empty— except for Mayor Prentiss. He welcomes them to his New World Order and introduces himself as President Prentiss. Dun dun dun… Get ready for the sequel, Shmoopers.