After vanishing out of his hotel bathroom, Joe finds himself in a much hotter and dustier version of the town, where something like a sandstorm is in progress. Suddenly - is it some kind of hot flash mirage? - Tom X appears wearing a tux. Joe wonders if they're both dead, but Tom knows Joe isn't that lucky: he's being saved. Joe wakes up in a white room, strapped to a cross-shaped table, covered in electrodes, IVs, wires and tubes. Tori's voice welcomes him back. Things have gotten off track, but they're going to fix his problems. The only downside? It's going to hurt... a lot.
Meanwhile, a desperate Janet has ripped Joe's room apart down to the studs, alarming Erika. Back in the white room, Tori's voice explains that there are a few options when it comes to Joe's formal re-education. Option one, Joe comes back to the Program. Option two, his body can't take it. No matter what, Joe will stay in this room until his re-education is complete, and as long as he's considered an asset. Because as Joe well knows, no one ever leaves the Program.
Joe flashes back. Dressed in a tux, Tom walks him through the hotel, introducing his new family, as men in blue coveralls wheel Charlie, Moira, Tori and Bill in on stretchers. Tom stops at Joe's room, the one where he was "reborn." Joe's greatest obstacle this time around won't be his mind, but his heart. At this moment, Janet is wheeled into her room. Joe finds himself back in the white room, where he's interrogated by Tori's voice. Is Janet really worth throwing away everything he believes in? What about the harm he's causing? What made Joe turn against the Program in such an aggressive manner?
Meanwhile, Kat and Renbe have made it to San Nicasio, somewhere in South America. The psychiatric hospital there looks a bit like a 19th century gulag, and hospital administrator Raul Samper turns down their request to interview Dr. Angela Barragan - because she's not a doctor, but a criminally insane patient. Apparently Dr. Barragan was a dedicated Peace Corps worker, until she poisoned the town's water supply, then told the women and children that God wanted them to drink. Rolling with the punches, Renbe bribes Samper for some time with Angela.
It's not long before an orderly is leading Kat and Renbe to Angela's barred cell. Having heard that Angela has to wear a straightjacket because she likes to throw feces, Kat pushes Renbe ahead. Strangely, Angela talks to the surveillance camera throughout the interview. She claims not to recognize the people in Renbe's Shanghai Palace photo, and instead babbles on about wanting churros from a particular shop at a particular address. Realizing that Angela will give them nothing more until she has her churros, Kat pulls Renbe out of the stinky cell as the camera closes in on them.
Struggling to fashion a crutch out of a broom, Charlie curses, drawing Bill's attention. Bill tries to joke around, so Charlie joins in, asking Bill if he remembers Joe saying they were each chosen for their potential. Charlie thinks it can't be true - after all, what kind of potential does Bill have? He's a donut hole. When Bill can't think of a retort, Charlie laughs, claiming Bill has proved him right. Hanging his head, Bill leaves.
As the camera sees all, Moira adds to her conspiracy wall: Joe eliminated? McNair isn't sure if Joe's been eliminated, but he's not happy that Moira hasn't spoken to him since she heard about his file. Moira's the only person McNair has told about what happened in Iraq, because she sees him for who he is on the inside. Moira wants to know if he would have told her if not for the file. Although he could have lied, McNair claims he told the truth because he wanted her to know him completely. Even thought he's ashamed of what he did, he's not going to run from it anymore.
As Moira cries alone in her room, Janet returns to Joe's room to study the portrait he drew of her. She grows teary-eyed, crumples the portrait and laments, "I trusted you." Meanwhile, back in the white room, Tori's voice implores Joe to return to the Program. The world needs him, and the way out is the way through. Joe shakes his head and screams in pain, seeing a vision of Janet sponging off his head. Tori wants to know how Joe can selfishly let Janet stand in the way. It's not going to end well. Joe screams out to Janet, asking her to wait for him. Janet reminds Joe that he can't go back, and he has to accept.
Dressed in a nurse's uniform, Tori enters the white room to sponge off Joe's forehead. He wakes up groggy and confused. Who is she again? Tori re-introduces herself, asking Joe if he thought she was dead. He only knows that he's supposed to remember her, maybe because she's supposed to give him the Program's instructions. Pleased that Joe's making progress, Tori reminds Joe that no one can ever leave the Program.
Dressed in his clothes, Joe finds himself walking down a long hallway with Tom. Only a very few test subjects show as much potential as Joe, so he's been summoned to a meeting with the Director of the Program, Angela Barragan. Angela greets Joe as Father Tucker, the most promising candidate they've had in years. Joe is the future of the program - but is he the ultimate team player? Joe says he is.
While Kat checks the address Angela gave them to find churros, Renbe wanders off towards a shrine, set up on the gate of a Catholic church. He's stunned to find a photograph of a younger and hairier Joe, a.k.a. the missing Father Tucker. Angela didn't want them to find churros after all. Soon, Kat and Renbe are meeting with Father Luis, who explains Joe was a pastor at the church for five years until the day he was abducted by government agents. When Luis produces a photo of Joe being dragged off by guys in blue coveralls, Renbe pulls out his Shanghai Palace photo. Luis is relieved to think that Joe's still alive - a miracle!
Bill pours himself a stiff drink at the lobby bar, delighted to discover a pack of unfiltered cigarettes. Thanking the camera for reading his mind, he lights up and waves for Erika to join, but she claims she's busy. When Bill points out that no one in the town is busy, Erika admits she doesn't want to join him. Now that Joe's gone, Bill is no longer useful. In fact, he's more like "a boil on her ass that won't get lanced." If he died, would anyone in the town give a rat's ass? Erika sidles off, leaving Bill to mutter over his scotch.
Nurse Tori is standing by in the white room when Joe regains consciousness. He's surprised to see she's a nurse now, so Tori explains that she's whatever the Program needs her to be. Her father was right - the Program has given her a vocation. Joe gets worked up: he had a vocation once too, until the Program took it away. Tori questions Joe's commitment to his vocation. Was it really so strong, considering the way Janet has shaken his commitment to the Program?
Joe flashes back to an event in his hotel room. Still long-haired and wearing his priest's collar, he aims a pistol at a guy named Ulrich, who pleads for his life. Joe aims his gun at the camera, asking if "they" want him to kill Ulrich. Finally, Joe shoots and kills Ulrich, then proceeds to the bathroom where he takes off his priest's collar. Dressed in his tux, Tom enters to meet Joe for the first time. Introducing himself as Joe's mentor, Tom tells Joe that he's ready to continue, then tasers him into unconsciousness.
Kat and Renbe return to Angela's cell to press her for information on her own kidnapping. Angela freaks out, screaming to the camera that her doctors told her she wasn't kidnapped, nor "part of the seven," nor indoctrinated into that Program. She had a life before they left her there to rot. But could there be a method behind Angela's madness? She attacks Kat, pushing her against the bars and telling her to "find the town and you'll find the program," before the orderlies come to strap her down.
Bill retires to his room to appeal to the camera. He thinks his captors have made a mistake - what could they possibly want with a donut hole like him? Crying that there's nothing special about him, Bill begs to go home. McNair finds Moira erasing her conspiracy wall, and tells her to stop. Moira refuses; it only meant something to her when he thought it was important - when he thought she was important. McNair kisses Moira in an attempt to show he still cares, but she insists that he leave. If he only knew...
Back in the white room, Tori tells Joe that time is running out. The love he feels for Janet is going to destroy him. Joe plunges into a series of hallucinations, screaming his refusal to give up Janet. Tori begs Joe to come back and accept his fate, but in his dreams, Joe kisses Janet. When the kiss is over, Janet reminds him the only way out is the way through. Joe knows the real Janet would never say something like that - this Janet knows Joe can check out, but he can never leave.
In the lobby, Moira wraps Charlie's leg, which is healing nicely; the Night Manager serves drinks; and Erika muses that Janet's dossier reveals she is who she says she is. Bill is just about to join in when McNair comments that the more likely collaborator is Bill. When Charlie insists that's impossible and everyone agrees, Bill retreats to the bus stop at the edge of town to sulk. He's about to light another cigarette when his matches blow away. Bill follows them, surprised to find that he has passed the edge of town. No Pain Wall! At first he's excited, but when he realizes he has nowhere and no one to go to, he trudges back to town. Returning to his hotel room, he gets on his knees in front of the camera - has he proven himself?
After a break, Kat and Renbe return to the hospital, hoping to find Angela, but she's already disappeared, and Samper won't help. Kat stalks off, determined to inform the police. Renbe puts on the brakes - they're not even supposed to be in the country! Besides, he has to go home and make a life with his daughter. Kat takes hold of Renbe. They're so close to finding Janet, and Megan needs her mother more than her father. They're going to keep searching until they find Janet and the truth. Kat seals the deal with a passionate kiss.
Back in the white room, Joe groggily looks to Tori on one side of him, and Janet on the other. Suddenly, alarms sound: Janet had pulled the trigger in his fever dreams, and Joe's flatlining. Tori screams out a code blue, and a team of doctors rush in to resuscitate Joe, as he steps forward free of wires and tubes to watch himself on the table. Joe tries to speak to a panicked Tori, but she can't hear him - only Tom X can. Does that mean he's dying? Tom outlines the choice: Joe wants to live, but he also wants to leave the Program. As Joe already knows, there's no such thing as free will. After all, no one chooses the Program; the Program chooses you.
Joe finds himself amidst the dust storm, standing with Tom, just like at the beginning of tonight's episode. Since this is the last time they'll be seeing each other, Tom offers his hand to shake. Death is indeed final. Joe shakes Tom's hand, then pulls him into a heartfelt hug. As the camera speeds away, Tori's voice can be heard through the ether, asking Joe if he can hear her. But the white room is now empty, and the door slams shut...