It's a cold night, pouring rain, and Janet is stumbling down the middle of a deserted woodland road, beaten and bruised. Suddenly Joe appears beside her to ask where she's going. Janet doesn't know, but she does realize she's hallucinating and Joe's not really there. When Joe disappears, Janet's eyes roll back into her head, she sinks to her knees, then passes out unconscious on the yellow line.
Some time ago, Renbe returns home to the new apartment he just moved into with a younger, more carefree Janet. Frustrated after years of writing novels with no success, Renbe has hatched a plan to cash in his chips and buy a 36-foot sailboat, despite the fact he doesn't know how to sail. Smiling to herself, Janet gently breaks the news that might impact Renbe's hasty plan: she's pregnant. Renbe freaks out and starts yelling. Janet may have thought he'd be happy, but she was dead wrong.
Janet awakens from her feverish flashback in a hospital bed, hooked to an IV and monitor. She rips out the tubes, and looks out the window, relieved to see the San Francisco skyline. She's just trying to sneak off when a nurse orders her back in bed. Janet refuses, insisting she needs to see her daughter. Before long, orderlies descend to force Janet into bed, as kindly looking Dr. Lemchen explains she was found four days ago, wandering on Highway 101. Janet will only be permitted to go home once they're sure she's alright. The nurse plunges a syringe full of sedatives into Janet's arm, and she passes out, crying for Megan.
When Janet wakes up, Detective Gomez is standing beside her bed. Refusing to answer his questions, Janet demands to know when she can see Megan. Lemchen promises she can as soon as she's up to it. Gomez asks about the town, and about Renbe, whom Janet hasn't seen since he abandoned her years ago in the middle of the night. Gomez shouldn't worry about Renbe; he needs to concentrate on finding Janet's kidnappers, and figuring out what happened to her fellow captives. Janet quickly becomes agitated, so Lemchen sedates her again. As she starts to fade, Janet advises Gomez to find the town - then he'll find The Program.
Somewhere in Morocco, two burka-clad figures hurry through a crowded marketplace. Moira stops, pulling aside her face veil; she can't do this. Indicating cops around the perimeter, Erika hisses. They have no choice. They agreed to do whatever's necessary to maintain their freedom, and she'll die before she's locked up again. Moira wearily agrees to Erika's plan to find a place to stay, unaware that the cameras are already watching their every move.
Kat and Renbe's rental car breaks down on the side of an Arizona highway. They wave to a speeding Mustang, but it speeds past. In the passenger seat, Bill wonders if they should have stopped, but Charlie knows they can't take any chances, and there's no one they can trust. Besides it's only a matter of time before the Mustang is reported stolen. Meanwhile, Gomez calls Renbe with news of Janet's return. Elated with the good news, Kat envelops him in a hug.
Dr. Lemchen wakes up Janet to introduce Dr. Andrea Adams, whom we immediately recognize as The Director! Of course, Janet has no idea, but she smells a rat when The Director starts asking questions about the town. Later in the hallway, The Director explains to Gomez and Lemchen that Janet has been through serious trauma, which has made her delusional. Right now she must remain in the hospital where she won't harm herself or others, and can't be reunited with her daughter until her mental state is confirmed. Listening from her bed, Janet hears every word.
Charlie and Bill abandon the Mustang on a desert road. Bill's not sure they should have left the town in the first place; at least they had food and a place to sleep. Charlie reminds Bill that he left out the part where The Program was going to kill them - remember when Ulrich's head exploded? If the experience taught Charlie anything, it's that he's now willing to do whatever it takes to survive. Meanwhile, Janet pretends to take the drugs the nurse gives her, later hiding them in her sheets. One thing's clear - Janet's hatching a plan.
After flying back to San Francisco, Kat and Renbe hop in a cab headed for the hospital. Renbe's relieved the whole thing's over, but Kat's not so sure. Renbe explains that he needs to visit Janet to apologize for everything he's done. And he needs to apologize to Kat, since they're at rock bottom, no jobs, no money, no place to live. Claiming she's not sorry for everything that happened, Kat forgives Renbe with a passionate kiss.
Renbe quickly becomes enraged when the receptionist tells him there's no Janet Cooper registered at the hospital. Kat spies Gomez and several cops approaching, so Renbe grabs her and runs into the hospital, just as a fully dressed Janet pops out of bed to beat her nurse to the floor. Running through the halls, Renbe spies Janet making her escape, just as he and Kat are beset by blue coverall guys. Renbe yells, "Don't let 'em get you," as he's tasered into unconsciousness. Luckily, Janet makes it out of the building.
In her office, The Director plays back the tape of her hospital interview with Janet for Joe, as proof of her promise that Janet wouldn't be harmed. Still, Joe points out, Janet's not free. Even though he knows Janet's fate is in his hands, he also knows she'll never give The Director the information she wants, despite all methods of persuasion. Insisting this is one fight The Director can't win, Joe leaves. The Director slumps in her chair, looking beaten as the Night Manager appears on the monitor to announce that another problem has cropped up.
Incensed that Janet, Kat and Renbe have disappeared into thin air, Gomez puts out a wide net APB. Meanwhile, under cover of night, Janet runs the stairs to her mother's house, where Edick meets her at the door. Without pausing to say hello, Janet rushes to Megan's bedroom, crying with relief to finally be reunited with her daughter. Megan rubs her eyes and asks Mommy if this is a dream, then rolls over and goes back to sleep.
The Director struts into the boardroom of The Mansfield Institute, apologizing unapologetically for calling an emergency meeting in the middle of the night. There's a situation. No one seems to mind except for an imperious man with long, white hair, who's concerned that The Director has put The Institute in grave jeopardy. She has messed up beyond the purview of her directive. Fighting back, The Director accepts full responsibility for her actions, but if they don't act immediately, they may let the most important Program participant ever slip through their fingers. And how dare they question her judgment! The white-haired man backs down, inviting The Director to proceed with the presentation of her plan.
Janet has a tearful reunion with her mother. She knows mom thinks she's crazy, but she's not. When Eleanor offers her arms, Janet melts into them. She's so tired, and just doesn't want to lose Megan again, and what's she gonna do? Just as Eleanor promises they'll figure it out together, the phone rings. Eleanor speaks to her old friend The Director in the other room. When Eleanor insists she won't give Janet up, The Director cajoles. Eleanor must know in her heart that this isn't about any of them; they made a commitment a long time ago.
Edick carries Megan downstairs and loads her and Janet into a sleek Mercedes. Eleanor assures that everything Janet said is true, but there's no time to explain how she knows. She prayed this day would never come, and it has. Now it's time to leave. Meanwhile, blue coverall guys lock a hooded Kat into a cage, surrounded by other cages in a fenced lot, circled by armed guards. Screaming, Kat takes off her hood, shocked to discover that the guy in the cage next to her is none other than... Ambassador Fairchild!
Back at The Institute, The Director and her Night Manager enter the white room where McNair is screaming, strapped to a table and riddled with wires and tubes. The Director explains the reason McNair is in such dire straits: there's a serious situation happening. Several guests have disappeared. McNair might think he's helping his friends when in fact, he's doing the opposite. Although The Director admires his compassion, it makes the procedure he's amidst necessary. The Director gives a signal and leaves McNair to scream his head off in a misery of pain.
Lounging around a campfire in the middle of the desert, Charlie muses about the changes he's been through while in captivity. He and Bill are lucky to have a second chance. Even if they can't go back to their old lives, aren't they both ready for a change? Bill agrees, then suggests they get some sleep. When he asks Charlie if he misses Charlotte, Charlie takes pause. He never mentioned his wife's name, so how did Charlie know it? Unbeknownst to Charlie, the camera is already upon them.
On the road, Edick tells Janet that Eleanor has been trying to protect her from "them," and he did, too. He never thought she'd be abducted, and he's sorry for it. It may be hard for Janet to believe, but Eleanor loves her and she always will. He pulls the car over at a motel, carries Megan inside, and urges Janet to sleep; they have to leave before daylight. Despite her best intentions to remain vigilant, Janet curls up beside her daughter, and passes out, to dream about Joe in fitful flashbacks.
The next morning, Janet wakes up alone in the hotel room. Tearing up, she looks to the camera in the ceiling. Resigned, Janet finds the room key in her Bible and goes to the door. In another identical room, Joe wakes up, finds the key in his Bible and exits into the hallway, where Renbe looks freaked out. He instantly recognizes Joe, calling him "Father," and demands to know what he's done with Janet. Just as in Episode 1, Joe warily explains that he just woke up five minutes ago.
When Joe and Renbe hear panicked "guests" beating on their doors, they yell, explaining the room key in the Bible thing. Charlie, Moira, Erika, McNair and Bill all wake up in their identical rooms, and get their keys out of their Bibles. Everyone boards the elevator and heads for the first floor. It isn't until the elevator doors open that we realize Joe and Renbe are back in the same town in the same hotel with five newbies, where a dour Tori has been installed as the new Night Manager.
Janet and the rest of the usual suspects (Bill, Erika, Charlie, McNair and Moira) exit their elevator to find themselves on the deck of a huge oil tanker in the middle of an unknown dark gray ocean. Wearing his eye patch at a jaunty angle and looking every inch the sea pirate captain, the Night Manager ironically welcomes them to Level 2... whatever that means.