A man wakes up from vague memories of a former life, and finds himself in the middle of a desert. There is nothing around as far as he can see, but he hears gunshots over the next ridge. He goes to check it out and sees a man fleeing from armed men with guns. The man goes to the escapee's aid and carries him to a cave. The escapee tells him to go to 554 and tell them something, but then realizes that the newcomer isn't from around here and that he's a miracle. He says "Be seeing you" and then collapses, dead.
The newcomer buries the escapee and sets out across the desert. He finally comes across a community, each building the same as every other. He enters and finds a taxi. The driver asks where he wants to go but informs the newcomer that there's no railroad station: he's local only. The driver explains that they're in the Village. Frustrated, the newcomer jumps out and follows the sound of music to a bar, Club More, and notices a woman nervously watching him. The newcomer goes to her and she invites him to dance. She says that he's in the Village and wonders if he's sick. A patrolman with a dog comes in and the newcomer runs back out to the taxi and tells him to drive anywhere.
As they drive, the newcomer sees a photo of a young girl, and the driver says she's 832. The newcomer asks him to take him to 554 and the driver obliges. He knocks on the door and a neighbor directs him to a nearby café where 554 works. The newcomer goes inside and 554 offers him a selection of wraps and seems surprised that he'd want anything else. He orders coffee and gives her the old man's message. She identifies the man as 93 and the newcomer says he was told to find her. 554 doesn't want to get involved and says 93 was just a drunk. When the newcomer tells her that 93 got away, she admits she didn't believe. As more security patrols come by, 554 tells the newcomer to go out through the back. He flees out onto a ledge as a man in a white suit watches below, holding a hand grenade. The newcomer notices him and jumps off into the street below.
As if in a dream, the newcomer sees the man in the white suit, who insists that the newcomer is Six and the truth is inside him. Six wakes up in a hospital bed. A doctor, 313, comes over: she's the woman from Club More. She tells him he's been sleeping for a while and Six admits that he thought he was dying. 313 tells him not to fight it and says that he's going to be taken home.
Six is taken to an office where the man in white, Two, is waiting for him. When Six wonders why they're keeping him, Tw points out there are no locked doors. He then asks why Six was in the mountains, and Six admits that he was lost and has no idea how he got there. He insists that he's not Six and Two asks for his identity papers. Six discovers there are identity papers confirming that he is Six, but he refuses to answer any questions about 93. When he asks to be taken back to New York, the man informs him there is New York: there is only the Village.
Six is driven to his new home: a comfortable flat with all the amenities. Six recognizes that it as his apartment from his original life. He refuses to sign for anything and goes out into the Village. As he goes out, there is a broadcast about the missing 93, saying he was mentally disturbed. Six goes to a shop and tries to buy a map but there are only locals. The owner points out the local attractions and calls Six by name, despite the fact they've never met.
Six goes outside and 313 comes over to talk to him. She asks where he's going and warns that he won't get far. She wonders what she can say to stop him and he demands the truth. She tells him the truth is that he's one of them. Six steals a taxi and drives out of town into the desert. When the road ends, he climbs up into the surrounding mountains but the landscape stretches on forever.
As he pauses for breath, Six has a brief flash of memory.
Six is in a restaurant in New York as a woman asks to borrow his phone. She leaves a message and makes small talk with Six, and then goes. Six runs after her and asks for his phone back. She notes he's carrying alcohol and figures he's having a party, and he invites her to come. However, he then admits he was lying and says that he's celebrating... escape.
Six collapses from the heat and 313 drives out to return him to the Village. He wakes up en route and she notes he was talking to someone. He wonders why she's so interested in his non-existent life, but 313 insists she wants to help him with his delusions. She can't understand why he'd want to leave. Six explains that he met a woman and invited her to his apartment, but admits he doesn't remember what happened after that.
In the VillageTwo opens a locked case and takes out a bottle of pills. He removes a few and takes them to a woman's bedroom.
The taxi driver, 147, is at home with his wife. They receive a letter summoning them to the clinic for an appointment with Two. At the bottom it says something else.
As they arrive, Six asks why they want to know where 93 is. He figures that 313 was sent to get him and trick him into talking. She notes that he doubts everything but warns that his paranoia is part of his condition. Six insists that it's no condition and he's being held against his will. Six takes a bus to 93's apartment and searches the place. He finds a number of empty wine bottles in the cabinet, and one bottle has a message in it. As he starts to read it, Two and his son enter. Two notes that he finds it odd that Six is there if he claimed he never met 93. Six insists that the Village is not all that there is and 93 knew it as well. Two dismisses his concerns as paranoia and fantasy, and says that Village citizens are free to do what they want, contented and hopeful. When Six insists he wants out, Two warns that there is no out, only "in." Six wonders why the guards were shooting at 93, and believes he found something. If 93 can do it, Six insists that he can too.
Six goes to see 554 and shows her the paper from the bottle, which has a drawing of Big Ben. She finally relents and says that 93 said the drawings were from his other life. 554 insists that's all she knows and that Six has to leave her alone now.
147 and his wife go to the clinic, bringing a cake with cherries, and meet with Two and his son. He presents them with medals for service to the Village, and then asks about Six, and 147 admits the man was strange. Two assures them that Six has been dealt with. He then asks after the cake, which was part of the summons.
Later, Two informs the citizens that they found 93's body in the mountains. At the diner, Six convinces 554 to meet him with him at his flat. She explains that 93's dreams meant that he had another life, and he started talking of how they were all prisoners. She shows him a drawing of her own, of the Statue of Liberty. She explains that there are others who have similar dreams, and Six promises that she's safe with him and he'll see her at the café tomorrow.
Two brings pills to his comatose wife and sits at her bedside. He feeds her the pills and then turns as his son 11-12 comes in. The boy asks why Six is so convinced there is another place, and Two explains that for people like Six, a simple life isn't enough and they want to escape it. He calls 11-12 over, kisses his wife, and pats his son on the shoulder.
Six goes to the gravesite where 93 is to be interred and remembers burying him in the desert. 313 comes out and he wonders what she's doing there. She admits she's there to find out what he's doing there. Six asks her to lie down next to him and she finally gives in. They look up at the sky together and Six talks about the billions of stars and what they represent, and wonders how the Village can be all there is. 313 suggests there might be another Village out there somewhere Six mentions names of famous individuals of history that his teacher Mrs. Radcliffe taught him. 313 insists none of them exist and Six continues to question her, and she wonders if he's trying to trap her. She admits that she's trying to trap him and asks about the woman from his memories.
Six tells the woman that he resigned today and is celebrating alone. She introduces herself as Lucy and he says he'd like to get to know her. She suggests that maybe she can, possibly tonight.
Six wakes up in the morning as 93's funeral procession passes. Six goes after them and realizes that they didn't find 93's body. He insists that 93 found the way out, but Two explains that Six has to believe that to convince himself there's a way out. Six turns and leaves as 11-12 considers Six's words.
Six goes to the café and 147 is waiting outside. He suggests that Six might need a ride, and he's being nice just to be nice. Six is skeptical but 147 says that he'll always be there if Six needs him. Six goes toward the café and hears a news broadcast about traffic. He's not sure if it's a piece of his missing memory. As the broadcast talks about a gas leak, the café explodes and Six and the others outside are blasted to the ground.
Six remembers lying on a city street, and a woman on a security camera talking of snuffing a man out with a pillow.
Six recovers conscious and finds a badly injured 554. She thanks him for the chance to meet him and hopes that they can escape together. She tells Six that 93 said to "follow the towers." The medics take 554 away and Six looks out at the two glass towers rising up out of the distance.
At the hospital, 313 tends to 554 and the other injured Villagers. Six arrives and asks the doctor what happened, and 313 says he should have stayed away from 554. She admits that she's scared and warns that sometimes things happen, but eventually they settle down. 313 tells Six not to make things worse and walks away.
554 dies and is taken away, and Six remembers his promise to keep her safe. He walks away and goes to Palais Two. He shouts out, blaming Two for killing 554. He vows to escape no matter what. Inside, Two settles down to eat his cherry cake.
Six runs to the glass towers but a large white sphere springs up from the sand and covers him.