A man awakes in an isolated desert community called the Village with no idea of how he got there. He is designated Six, as everyone in The Village is referred to only by a number and the Villager's administrator, Two, attempts to assimilate him into the community.
Number 6's feeble attempt at escape soon comes to an end and he is returned to the Village. There he is introduced to Number 16 who claims to be his brother. Number 6 is understandably skeptical about it all and has no recollection of 16. He also learns that he is a bus driver by profession, giving tours around the the Village. When he comes across a ship's anchor in the middle of the desert he begins to think there may be another way to escape. We learn more about Number 6's life in New York City and that he had resigned as an analyst with a security company that reviewed CCTV footage from around the world. It is also clear that he was under observation even then. As Number 6 goes from what he thinks is reality to waking dreams, he is no longer sure what is real and what is imagined. Meanwhile, Two tries to deal with his son's growing sense of rebellion.
Number 2 asks Number 6 to work for him as an agent to locate dreamers, that is those who dream of a world other than the Village. Number 6 is under no illusions however and while he agrees to work for him, he does so only to hopefully gain some type of advantage over him. He's paired with 909 and is placed as a teacher of surveillance in a school to observe Number 1955, also a teacher. He uses his position to his advantage by asking his students to find out what exactly is going on. He also learns about Number 1. Life becomes more complicated when 303 learns that he is working as an agent and assumes that she was one of his targets. 11-12's secret is revealed.
Six is forced into attending a matchmaking service, the matchmaker, 1891, who appears unwanted on his television screen. He is matched with a blind woman named 4-15, who looks exactly like Lucy with whom Six had a sexual liaison in New York. Six is convinced that she is indeed Lucy, although 4-15 appears not to know anything about life outside of The Village. Both Two and 11-12 ask 313 for assistance on specific matters, with Two and 313, she knows that he is aware that she is a dreamer, the reason why she feels she needs to help him. But she still has to decide if what he asks her to do is worth her long term happiness. Meanwhile, all the talk around The Village centers on the mysterious holes that have been appearing in The Village, which Two dismisses as weather related anomalies. To combat these, pigs are distributed to residents, as swine breath is deemed to be a atmosphere stabilizer.
Six discovers he has a twin... who attempts to murder Two. 313 battles with her inner demons and 11-12 seeks the answers to his dilemma.
Six's time runs out when the order is handed down for his execution. Two suffers a personal loss and all is revealed.
