Janet is walking down the highway in the rain. Joe appears beside her and asks if she knows where she's going. She insists that he's just in her head and he says they both know where they've been. Janet finally collapses onto the road.
Renbe arrives home as Janet prepares their apartment. He complains about all of his recent rejections and she says he should take a break, and Renbe suggests that he sell most of what he knows and buys a sailboat. Janet tells him that she's pregnant, and Renbe demands to know how and when it occurred. He informs her that he isn't happy.
Janet wakes up in a hospital bed. She goes to the window and discovers that she's in San Francisco. Janet leaves her room and a nurse refers to her by name, assuring her that she's safe. When Janet tries to leave, the staff restrains her and Dr. Lemchen tells her that they found her wandering on the highway. She insists that they're all part of the Program, and they place her in the bed and sedate her as she yells for her daughter.
Later, Janet wakes up and finds Detective Gomez waiting to interrogate her. He tries to find out more about where she was and who was with her, but Janet isn't able to give convincing answers. Gomez asks if Renbe has contacted her, and Janet insists she hasn't seen him since he abandoned her and Megan. She insists he needs to find the others and gives their names, but Dr. Lemchen sedates her.
In Morocco, Erika leads Moira through the crowds. They avoid the police and Erika insists that no one will lock her up again and she'll do whatever she can. Erika leads them to find a place to sleep.
Bill and Charlie are in a stolen car and unknowingly drive by Renbe and Kat, who are stranded after their car has broken down. Charlie insists that they can't trust anyone. Meanwhile, Renbe gets a call on his cellphone from Gomez, who informs him that Janet has turned up alive.
When Janet wakes up, Dr. Lemchen brings in Dr. Andrea Adams to see her, unaware that she's the Director. Afterward, the Director tells Gomez that Janet is delusional and she should not be reunited with Megan until they confirm her mental status. Lemchen agrees and they make plans to have her transferred to a special facility.
When their car breaks down, Charlie and Bill start walking. Bill suggests they should have stayed in the town, and Charlie points out that their captors were willing to kill Ulrich. Charlie says that he's learned that he'll do anything to survive.
The nurse gives Janet pills to help her sleep, and warns that she'll force Janet to take them if she refuses. Janet seemingly takes them, but spits them out once the nurse leaves.
Kat and Renbe fly back to San Francisco. When Kat wonders if it's over, Renbe says that he's going to visit Janet to make sure she's okay and to ask for her forgiveness. Kat warns him that they're at rock bottom with no money or jobs, and they'll have to start over from scratch. When Renbe admits that he's sorry it all happened, she tells him that she isn't and they kiss.
Janet knocks out the nurse when she comes to see her, and then runs out the door. Renbe and Kat arrive at the hospital, but the staff insists that there's no Janet Cooper there. They notice that the security is on alert and realize something is going on. They spot Gomez and the police approaching and run for it. Meanwhile, Janet slips out of the hospital and sees Renbe and Kat down the hallway. Before she can approach them, men in blue coverall taser them unconscious. Janet keeps on going and gets out.
Later, Joe and the Director watches video of her questioning Janet in the hospital. On the tape, Janet admits that she has feelings for Joe. The Director tells Joe that Janet is alive and unharmed, just as she promised. Joe point out that Janet isn't free, and asks what will happen to her. The Director tells him that it's ultimately up to him, and says that they have ways to get the information from him. Joe warns that nothing she can do will get the information from him, and warns that the escapees didn't tell him anything. As Joe is taken out, he warns that she won't win this one. The Night Manager, Neil, calls to tell her they have a problem.
Gomez realizes that he's lost Renbe, Kat, and Janet. He puts out an APB and warns that he won't accept any excuses.
Janet goes to Eleanor's house and finds Edick there with her mother. She runs upstairs to Megan and assures her daughter that she's there, and then lies in bed with her.
At the Mansfield Institute, the Director convenes an emergency meeting and is surprised to discover that the Chairman of the Institute is there. He warns that the Institute has been exposed to extraordinary risk, but the Director insists that it's worth the risk. The Chairman warns that she's gone beyond her job requirements and they're not willing to continue supporting her efforts. The Director tells him to do what he has to, but that they can't lose the most important participant in the Program. She explains that she has guided the Institute for 25 years beyond all imagined limits, and refuses to have him or anyone question her judgment. The Chairman tells her to proceed.
Janet tries to convince Eleanor that what she's saying is true, and collapses into her mother's arms, crying. The phone rings and Edick comes in to let Eleanor know it's for her. Eleanor takes the call: it's the Director. However, Eleanor says that she won't let the Director take Janet again. The Director warns that it isn't about what any of them wish, but about the commitment they made. Eleanor hangs up the phone and has Edick get Megan, and then drive Janet and her daughter to the border. She then tells Janet that everything she's said is true, and that she has to leave. Janet takes Megan and goes with Edick.
Kat is taken to a prison camp and locked in a cage with other prisoners. She realizes that Franklin Fairchild is in the cage next to her, and he warns her that neither one of them will ever escape.
The Director and the Night Manager go to the white room where Graham is strapped in and tortured for information. She demands to know where his friends are, and warns that he is hurting them. She leaves as the torture continues and he convulses in agony.
Charlie and Bill set up a campfire for the night, and Charlie admits that he's not the same man he was when he arrived in the town. He points out that Bill isn't the same man, either, and Bill hesitantly agrees. Charlie figures they will both get a second chance, but warns that they can't go back to the lives they had. However, Charlie is ready for a change. Bill isn't convinced, and asks if Charlie misses his wife, referring to her by name. Charlie admits that he does, but then wonders how Bill knows his dead wife's name. Bill claims that Charlie told him, but Charlie isn't convinced.
As Edick drives Janet and Megan to the border, he explains that he's been working for Eleanor the entire time. He assures Janet that Eleanor does love him and wants what's best for her. Edick stops at a motel for the night and tells her to get some sleep. Once she's alone with her daughter, Janet tells Megan that she loves her and dozes off next to her. As she sleeps, Janet remembers everything that happened to her.
The next morning, she wakes up ion a different hotel room and discovers that Megan is gone. She looks up at the camera on the ceiling and wonders how they could do it. She then takes out a Bible from the nightstand and removes a key. Joe wakes up in a hotel room and finds a key in a Bible. He unlocks his door and goes outside. Renbe is in the room next door, and wonders where they are. Joe informs him that he only woke up five minutes ago and doesn't know where they are. Renbe says that he recognizes him as Father Joe and demands to know where Janet is. Janet emerges from her hotel room and finds Moira across the hall in what appears to be the hotel.
Throughout the hotel, other people pound on their doors. Joe and Renbe tell them how to escape. Janet and Moira find Erika, Charlie, Bill, and Graham as they emerge from their rooms. Graham walks by Charlie without a word, looking guilty. Charlie looks at Bill, who appears apologetic. Renbe hesitates but finally gets in the elevator with Joe and the other new arrivals.
The new arrivals emerge out into the lobby and Tori is there. She introduces herself as the new Night Manager and tells them to let her know how she can make their stay more comfortable. The original abductees emerge from an elevator and find themselves aboard a freighter somewhere far at sea. The original Night Manager is there and welcomes them to Level 2.