Joe is standing in a ghostly version of the town. He finds Tom waiting for him in a tuxedo, and wonders if he's dreaming and they're both dead. Tom admits that he's dead, but Joe is being saved. Joe wakes up and finds himself in a white room, strapped to a table and wired into a machine. Tori talks to him on the intercom and tells him that things are out of control, and they're going to have to fix the problem. She warns him that it's going to hurt.
Janet searches Joe's room but finds nothing to indicate how he disappeared into thin air. Erika comes in and tries to calm her down, and Janet wonders where they've taken him.
Joe wakes up again and asks for an explanation. Tori tells him that he's in re-education and he either comes back to the Program or he dies from the re-education process. As long as he's an asset, he'll be kept for re-education and no one ever leaves the Program.
Joe arrives at the hotel with Tom and watches as his six fellow captives are taken to their rooms. The Night Manager greets Joe, saying it's good to see him again. Joe goes to his room and says it's good to be home, and Tom warns that his heart will be his greatest obstacle this time.
Tori asks Joe what harm he will cause because he's choosing Janet over the Program, and wonders why she turned against him.
In San Nicasio, South America, Kat and Renbe go to the hospital to meet with Angela Barragan. Raul Samper, the hospital administrator, greets them and says that the hospital has declined their request for an interview with Angela. When they wonder why they can't talk to a physician, Samper explains that Angela is there as a patient. She's been a prisoner for 25 years and is considered criminally insane. When Renbe mentions the Program, Samper explains that Angela was a Peace Corps worker who poisoned a town's water supply. Renbe bribes Sampler to arrange an interview. They talk to the woman, who rambles on about food, nervously glances at the surveillance camera, and agrees to talk to them only if they bring her a churro from a particular shop. When Renbe tries to question her further, Kat pulls him out and warns him that Angela won't say anything until she gets her churro.
Bill comes in to see Charlie in his hotel room, where he's recovering from his gunshot wound. Charlie figure that Bill has no potential so there's no reason for him to be there. Unable to come up with a witty response, Bill walks away.
Graham goes to see Moira, who is writing clues on her wall. He points out she hasn't spoken to him since he admitted he killed a man in Iraq. She admits it's a lot to take in, and Graham says she's the only person he trusted to tell her. He points out he could have lied to her, but it's part of what he is and he's not going to run away from it. Moira breaks into tears and Graham leaves.
Janet goes to Joe's room and takes out the sketch he made of her. She looks at it and admits that she trusted him.
Tori tells Joe that they need him and he has to come back to them, for the sake of the Program and the world. He imagines Janet in the room with him, wiping his brow, and tells her that he loves her. Janet tells him to accept.
Tori, dressed as a nurse, comes in to tend to Joe. He wonders if she's real, and asks her to say out loud who she is. She admits she is Tori Fairchild, but Joe isn't sure if she's alive, or if he's supposed to remember her so she can give him the Program instructions. Tori believes he's been through re-education before, and reminds him that no one ever leaves the Program.
Tom takes Joe to see the Director, and notes that only a small percentage of subjects show the potential that Joe has demonstrated. A woman greets him, calling him Father Tucker, and says he is the future of the Program. The Director asks if he's a team player, and when he agrees, tells Joe that he's the future.
Renbe and Kat arrive at the shop address and Kat goes inside to check it out. Renbe wanders around the plaza and finds a nearby church gate with a "missing" poster of Joe, the man in their photo. When Kat returns, Renbe shows her Joe's poster. They go inside and talk to Father Luis, who explains that Father Tucker disappeared when government agents took him away for aiding the rebellion. He has a photo of the men in blue coveralls taking Joe, and they show him the photo of Joe in front of the Chinese restaurant. Luis confirms that it's Father Tucker, even though he doesn't know Tori and Janet.
Bill is drinking in the hotel bar and finds a pack of cigarettes behind the bar. As he lights up, Erika comes down and he invites her to join him. She tells him she has better things to do, and tat he's useless to her now that Joe has disappeared. Erika tells him that no one would care if he dies and walks away.
Joe wakes up again and Tori says she's whatever they need her to be. She explains that she believes her father recruited her, and the Program has given her a vocation. Joe yells that he had a vocation once, but the Program took it away from him. When Joe insists that hundreds of people relied on him, Tori questions his commitment to the church now that he wants Janet.
Joe is in his hotel room, shooting a man. Afterward, he removes his collar. Tom enters the room, says that he's ready to continue, and tasers him unconscious.
Renbe and Kat return to see Angela and show her Luis' photo. She insists her doctors said that she wasn't taken to a town as part of the Program. She breaks out of the straitjacket and attacks Kate, and screams at them to find the town to find the Program. They go to get Angela freed so they can locate the town.
Bill emerges from his bathroom and talks to the cameras. He asks if he'll ever get an explanation, and insists that he has no potential and they must have made a mistake. Bill breaks into tears as he wonders why they took him, but gets no response.
Graham goes to see Moira and discovers that she's erasing everything on her wall. She insists that it isn't important now that Graham doesn't think she's important. He assures her that she still is to him and tries to kiss her, but she begs off and asks him to leave. Graham reluctantly goes and Moira whispers, "If only you knew."
Tori warns Joe that his time is running out and his love for Janet will destroy him. She insists that he's the future of the Program and he has to let Janet go. Joe imagines that Janet is waiting for him at the church gate, and she tells him the same thing Tori is saying to him.
Charlie, Erika, and Moira are in the lobby discussing their situation. Erika says that Janet's dossier confirms her story, but Moira points out that the files may not be true. As Graham arrives, he suggests that Bill might be a mole. Unaware that Bill came in behind them, the others casually dismiss Bill as a mole because there's nothing to him. He goes to the edge of town and smokes, but drops his matchbook. The window blows it into the barrier and Bill chases after it. He realizes that the pain barrier isn't there and starts running out of town. However, when he realizes he has nowhere to go, he turns around and goes back.
Renbe and Kat return to rescue Angela, but discover that her room is empty. Samper explains that things happen and they've compromised his position with their questions. He tells them to leave.
Bill returns to his rooms and tells the camera that he stayed even when he had the choice to go. He gets no response.
Kat goes to the police but Renbe warns her that they're in the country illegally. Renbe is ready to give up and go home to be with his daughter. Kat figures that they took Angela because they're close to finding Janet, and Megan needs her mother. She refuses to let Renbe stop until they find the truth, for Megan and for both of them.
Tori tells Joe that they want to take away the pain. Joe remembers more of his life of a priest, and his confrontation with Janet when she threatened to shoot him. When he imagines her pulling the trigger, he has a seizure and flatlines.
As the doctors try to revive Joe, Joe finds himself standing behind them, unseen. Tom appears and Joe insists that he wants to live. He wonders if he has to choose the Program to live, but Tom warns that there's no free will and the Program chooses. Tom says it's time to go and they are back on the street again. As Tom fades away, he says that they won't meet again and embraces his friend.
In the white room, Tori calls out to Joe, who has disappeared.
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