A man awakes in an isolated desert community called the Village with no idea of how he came there. He is designated "Six" and the Villager's administrator, Two, attempts to assimilate him into the community.

Later, Six discovers that his brother is in the Village but isn't sure who he really is. Meanwhile, Two tries to deal with his son's growing sense of rebellion.

Six agrees to help Two by spying on his fellow Villagers. Meanwhile, 11-12's secret is revealed and 313 learns to fear her gift.

Later, Six meets a woman from his past while 147 endures family tragedy, and a natural disaster strikes the Village.

Later, Six's rebellions are no longer tolerated and he is sentenced to execution. Two suffers a personal loss and the truth will out.