The book starts in Prentisstown, where all men's Noise (thoughts) can be heard by everyone, and there aren't any women. Todd, 30 days away from his 13th birthday, at which point he will become a man, has been told that the Noise came with the same germ from the native inhabitants of the planet that killed all the women. But one day Todd starts finding out that everything he's known about his town and his planet is not what he's been told.
Ness opts to reveal the secrets to the reader as they are revealed to Todd, a technique that can be frustrating, but mostly works well. Most of the secrets are revealed (we think) by the end of this first book in a projected trilogy, but there's still plenty of suspense as to what actually happens to our hero and whether good will triumph over evil.