Joe wakes up on the town street, naked. Janet finds him and brings him into the hotel. The others gather and Joe finally explains that he doesn't know where he is. He appears to know what they mean by the Program, but then insists that he doesn't know who they are.
Later, Joe goes to the Shanghai Palace to get answers. Nobody responds when he gives the code phrase, and he discovers that the door to the command center no longer exists. When he asks where Tom is, the staff shows him a memorial photo. Joe addresses the cameras, and surveillance operatives watch him. Their supervisor, Liam Ulrich, arrives and demands to know why he hasn't been put in contact with the Director as he requested. Ulrich warns them that heads will roll if they don't do their job.
Janet is outside contemplating Joe's sketch of her when Erika approaches. When Janet admits she can't handle the constant changes, Erika points out that she's the only one who hasn't given in. She figures that their captors brought Joe back to try and break her, and they're scared of what Janet can do and what she represents.
Kat and Renbe have holed up in a cheap hotel in San Nicasio, and Renbe complains about the lack of foods. Kat points out that their credit cards are maxed out and their cell phones can't pick up any signals. She plans to get a job and get enough money to buy plane tickets back to the U.S. The hotel manager brings the police, who take Renbe away based on a San Francisco warrant on charges of kidnapping and murder.
Joe returns to the hotel and Moira offers her assistance if he wants to talk about what happened. She insists that he tell them what he knows when he's ready, and warns that the others don't believe that he's telling the truth about his amnesia. As she goes, the Night Manager comes down and asks if Joe is doing okay. There's an electronic beeping noise from the Night Manager's office, and he quickly goes to answer it. In his office, he activates a hidden electronic array. Ulrich contacts him and demands answers, and then puts the Director online. She discovers that the Night Manager has no idea what's going on and that he's the only officer on-site. Ulrich is surprised to learn that the replacement hasn't arrived, and tells the Night Manager to continue monitoring Joe and await further instructions.
Kat and Father Luis arrive to bail out Joe as a prisoner tries to take his shoes. Luis warns that he can get them across the border in coffins, but they have to hurry.
The Director calls Ulrich in and demands answers. She says they have a rare candidate for the Tenth Level, and has invested much of her personal time into the project. Ulrich isn't as impressed by her opinion of Joe, but she warns him not to let personal feelings affect his decisions. The Director sends him to keep an eye on the situation and returns to monitoring Janet.
At the Shanghai Palace, the captives gather and discuss their situation. Charlie wants to work with Joe, Bill thinks they should enjoy the situation, and Graham feels they should stay clear of Joe. Moira believes that Joe can help them get out, and can eliminate him later. Joe comes in and gets some food, and Charlie tries to get through to him, insisting Joe owes him for Charlie taking a bullet on his behalf. Joe isn't impressed and goes into the kitchen to make a sandwich. Janet goes after him and reminds him that he promised her that he'd help her escape. He doesn't believe it and when she touches him, he snaps. Memories of his re-education flash through his mind as he chokes her and then throws her over the counter and grabs a knife. The others hold him off and he runs off into the streets.
Father Luis drives the truck to the border. They avoid searching the coffins and let him through.
The prisoners return to the hotel and Graham wants to focus on keeping each other safe. Erika has read his file and says that he hasn't hesitated in the past about killing when he has to. Bill is ready to take a nap, until Erika suggests Joe might be in his room waiting for him. Charlie would rather keep Joe alive but Janet agrees with Erika and Moira and feels they should locate Joe.
The Night Manager calls in Code Red, and Ulrich contacts him to warn that he doesn't have the authority. He overrides the lockdown, but the Night Manager warns that the town isn't secure. Ulrich reminds him that the Director thinks Joe is an asset, and they can't disappoint her. The Night Manager is unable to locate Joe on the monitors, and Ulrich takes care of the situation until he can send support into the town.
The prisoners split up to search for Joe, unaware that Joe is on the hotel rooftop watching them.
Luis pulls off down the road and lets Kat and Renbe out of their coffins. Renbe admits that the entire thing sounds insane, and Luis says there have been villagers in the area reporting strange lights and men in blue. Before Renbe can get more information from him, a shot rings out and Luis falls down, dead. The men in blue close in and Renbe and Kat run off into the woods and hide in a ravine to lose their pursuers.
The Night Manager has decided he’s had enough and packs to leave. As he exits his office, he finds Joe outside. Joe demands answers and the Night Manager gives him the code phrase to access the command center. Joe explains that he has no idea what week they are in the Program cycle, and is surprised to have the Night Manager confirm that he’s been there since the beginning. He asks about Tom and is informed that his friend is dead. The Night Manager also confirms that Joe and Janet were involved. The Night Manager touches Joe, who goes berserk again, viciously beats him, and throws him through the hotel’s front window before running off. The others come to investigate and try to treat the Night Manager. They argue about what to do with Joe, and Erika and Moira want to go after him. Janet agrees but offers herself as bait over Erika’s objections.
The Director contacts Ulrich and demands an explanation. Ulrich assures her that they’ll soon remove the Night Manager, and warns her that Joe’s re-education wasn’t entirely successful. She holds Ulrich responsible for Joe’s actions and warns him that nothing of the sort can happen again.
As Renbe and Kat try to get out of the woods, Kat once more complains about becoming involved in something that she has no interest in, all for Renbe to help his daughter. He admits that he’s doing it for Megan and for himself, but that he loves Kat. She admits that she loves him as well and they kiss.
Janet finds Joe on the hotel roof, ready to jump. He asks her to stay away and explains that their captors have tampered with his mind. She tells him to fight it but Joe insists that he can’t and warns her not to come near. Janet approaches him, insisting that he can’t let “them” win. When she pulls him back, he grabs her and throws her over the edge, hanging onto her by the wrists. Janet begs him to fight it, and reminds him that the way out is the way through. Joe manages to regain control of himself and pulls her up.
The Director and Ulrich watch the encounter, and Ulrich insists that Janet is special. His superior agrees and informs him that he’ll be taking a direct hand in matters by serving as the new Night Manager.
Janet brings Joe down to the lobby and insists to the others that he’s okay. They disagree and move in to eliminate Joe. When Erika advances on Joe, Janet hits her once in the face. Erika backs away and tells her they’ll do it her way… for now.
Kat and Renbe make their way out of the woods and notice a dirt road. They follow it and find the town.
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