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.
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 wonders what secrets her past holds.
Six meets a woman from his past while 147 endures family tragedy, and a series of anomalous holes threaten to engulf the Village.
Six is seeing double when an evil version of himself launches an assassination attempt on Two. 313 struggles with her inner demons and 11-12 seeks answers to his personal dilemma.
Six's rebellions are no longer tolerated and he is sentenced to execution. Two suffers a personal loss and the truth will out.