A New Yorker who recently resigned from his job, awakens in a desert mountain location. He doesn't know where he is. He sees an elderly man being shot at, the elderly man who eventually dies of his gunshot wounds. The New Yorker thinks he will befall the same fate as the elderly man. The New Yorker makes his way into a nearby city - a desert oasis - and learns that everyone there is called by a number, and that this city is called "The Village". Although knowing it is not his name or his home, everyone is calling him Six, and he lives in an apartment in the The Village. The face of the authorities of The Village is Two, who tells Six that The Village is the only reality there is. Six is told he's a free man, but he feels like he's a prisoner in The Village. He believes the elderly man, who Six learns was named 93, knew that there was an alternate reality outside of The Village and found a way to escape, which is the reason he was killed. With the help of a waitress named 554, Six also learns that there are a few in The Village who also believe there is a world outside of The Village. As Six tries to figure out what's going on, he has a recurring memory of a situation in New York involving a woman named Lucy.

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 longer sure what is real and what is imagined.

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.

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. One of those holes is in 147 and 21-16's backyard. A tragedy occurs in their family because of the hole.

Both 313 and 147 mention encounters with Six that Six denies remembering. While 313 and 147 believe it's because Six is having a mental breakdown, Six soon realizes it is because there is a double of him wandering around The Village. Calling himself 2x6, the double, who is a vengeful version of Six, has the sole mission of killing Two. Despite his disdain for Two, Six wants to stop his double from accomplishing this task as he believes it will make him no better than those he despises. There is also a double of Two wandering around the Village, calling himself the Untwo or the Numberless, who has a different purpose. Meanwhile, Two discloses to 11-12 where The Village is located. 11-12 spends some one-on-one time with his mother, M2, for the first time in his life. She confirms and expands on what Two has previously told their son, which includes why 11-12 will spend the rest of his life in The Village. 313 is having nightmares and comes to face those nightmares directly when she finds a portal to another world. And Six begins to have a concurrent life as Michael with memories of Six. As Michael, he begins to understand who is sent to The Village.

The Village is expanding since there are more and more newcomers arriving. Unlike Six, these newcomers believe they are arriving from The Village as opposed to from another world. Six begins to feel increasing pain, and learns that he is beginning to die. Two explains to Six the nature of Village death, and that Six does have a choice as to his future. 313 increasingly understands that she has a life in another world, and has to control how that life affects her in The Village. She wants to do whatever she can to help Six in having a better future, as does 147. 11-12 also understands his place in The Village and takes steps to control his own destiny. Six believes that 11-12 may be his key to escaping from The Village. And as Michael learns the truth as to what is happening from Curtis and Helen including why Six has a memory of his other life whereas others in The Village do not, Michael has to make a decision as to Six's fate as well as those in The Village, most specifically that of 313. All of this is happening as an increasing number of holes appear in The Village and may consume its inhabitants unless a decision is made quickly.