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You only think you're free.
A man wakes up in a new place - a place he doesn't recognize, a place where people have numbers instead of names, a place called "The Village" where all traces of his former life are renounced as delusions.
6 wakes in the desert, where he sees an old man, 93, and several pursuers shooting at him. 93 is dragged into a cave by 6, where 93 tells 6 to 'go to 554' before dying. 6 buries 93 and wanders into the Village, where he meets 2 and is grilled about 93's location. He finds a confidant in 554, who is killed on 2's orders.
6 struggles to find allies to escape from the Village. 2 introduces 6 to his brother's family to convince him he belongs. As 6 begins to doubt himself, his brother admits to the façade and the pair make a failed attempt at escape. His brother drowns in the attempt—as 6's had many years ago—following an encounter with Rover, but 6 finds renewed faith. Meanwhile, 2 and 11–12 discuss the latter's apparent lack of childhood memories.
2 offers 6 the opportunity to become an undercover agent, spying on suspected dreamers. 6 accepts with ulterior motives. He works with 909, who is spying on him. 6 follows 909 into the Go Inside bar, where he finds him meeting with his secret lover, 11–12. Rather than allowing the relationship to be discovered, 11–12 kills 909. 6 blackmails 11–12 to help him rescue 313, who has been captured and sent to the clinic.
The Village Matchmaking Service targets 6, pairing him with a woman, 4–15. 6 recalls 4–15 from a brief encounter with his previous life, shortly before he was taken to the Village. 4–15, however, pretends that she does not remember 6. They become lovers and plan to marry until 313 intervenes. 4–15 reveals to 6 that she is indeed Lucy, the woman Michael knew in New York; 2 has brought her to the Village to break his heart and spirit. 4–15 apparently dies by jumping into a mysterious, bottomless pit; in a concurrent flashback to New York, Lucy is apparently killed by an explosion in Michael's apartment.
2 has embodied 6's animal desires in an identical double named 'Two Times Six'. 6 must find a way to reconcile himself with his desires or risk being manipulated by 2. Meanwhile, 11–12 confronts his mother, 313 sees more visions of her past, and 2 relaxes for a day as 'UnTwo'. In New York, Michael returns to Summakor to find answers. 11-12's mother reveals that bottomless holes appear when she is awake.
6 encounters new arrivals, which contradicts claims that no world exists. 2 shows off new houses, indicating the Village's expansion. This is later revealed to be to increased pressure on 6 to replace 2 to stop the holes from destroying the Village. 6 confronts 2 about the newcomers, but soon forgets as 2 reveals he has afflicted 6 with a disease that will kill him. 6 confronts 11–12 when he meets him at l 909's grave and again at Go Inside.
