At the Inostranka command center, Thomas tells Pearson to give the orders to pull his men off their posts so that his sleeper soldiers can capture them without a fight. When Pearson refuses, Thomas orders Aaron to shoot Pearson dead. He then tells Grier to give the order, but Grier warns that he doesn’t know the security codes that Pearson had. Thomas assures him that he doesn’t have to and gives him the codes to order the prison soldiers to stand down, and the sleepers quickly capture them.
In the interrogation room, Maya informs Sterling that her people don’t believe in investigation, but he’s unimpressed. When he notes that she murdered her boyfriend, William, to keep him from talking, Maya explains that she did it to keep him from doing harm. In response, the director shows her photos of the comatose airplane passengers and dares her to explain the attack on them. Maya insists that her people didn’t do it, but Sterling explains that Thomas planned the biochemical attack. Corporal Bell interrupts to tell Sterling that they’ve been ordered to proceed to the boiler room for the drill. Sterling refuses to leave and tells Bell to stay on post. When Bell reports to the command center to inform them of Sterling’s decision, Thomas realizes that the director is on-site and sends his men to get him.
Sterling continues the interrogation and insists that she hasn’t been in contact with Thomas or Sophia. When Sterling doesn’t believe her, Maya asks what she can do to prove she’s telling the truth. Sterling warns that there’s nothing she can say. Outside, sleepers open fire on Bell, who ducks for cover. He enters the interrogation room and warns Sterling, who takes Bell’s sidearm. They free Maya and shatter the one-way mirror, and hide in the adjoining room. When the sleepers enter, Bell and Sterling shoot them down. Sterling interrogates one of them and realizes that they’re there to free the detainees, and that Thomas is leading the operation in person. One of the wounded sleepers goes for his gun and wounds Sterling before Bell can kill him. Maya slips away in the confusion, and Sterling tells Bell that they have to stop Thomas from releasing the detainees.
At the White House, Martinez meets get an update from his staff on the decryption efforts and Michael’s escape en route to the supermax facility. Lee has returned and reports that he’s found nothing yet on Michael’s escape. Martinez is informed that Senator Lewis has arrived, and he goes to see her. She reveals that she knows her husband was helping to finance the Inostranka facility, and has discovered that it’s a prison. Martinez points out that she must have obtained the information illegally, and insists that it’s a matter of national security. Lewis refuses to let him hide behind those words and questions his integrity, and Martinez argues that she knows nothing about the situation and should deal with the problems in her home state first.
Michael brings Sean, Leila, and Samantha to a house where they meet with Sophia. She thanks Sean for saving Leila’s life, and explains that she and her people crashed on Earth 66 years ago. Since then she has been trying to get her people home through peaceful means. When Sean points out that kidnapping, shootings, and murder have inevitably followed, Sophia explains that Thomas has different intentions, and that he plans to bring the remainder of her people to Earth... where they will destroy the world as Sean knows it.
In another room, Leila meets with Michael and accuses him of lying to her. She asks for answers and Michael explains that he’s from a distant planet, NCG 253. When that planet could no longer sustain life, his people traveled to Earth to find a new home. When their vessel crashed, he escaped with some of the others and went undercover. Years later, he met Leila’s mother and covered up Leila’s existence. Michael admits that Leila is half-human and half-alien, and tells her that he’ll answer all of her questions in time. However, Michael tells her that she has to come with him, and Sean can’t accompany them. He insists that it’s Sophia’s orders, and Leila will have to choose between her lover and her family.
At Inostranka, Thomas sends more sleepers to capture Sterling. His people have 30 minutes to get out of Inostranka before the next shift arrives. Thomas then talks to the detainees as they’re released, and tells them that Sophia has left them in prison while she gained her freedom. He informs them that he and Sophia have split and that they can come with him instead of serving her by staying in prison.
Sterling and Bell get to the command center and take out the remaining sleeper guard. They realize that Pearson is dead and the communication gear has been destroyed. While Bell tends to Sterling’s wound, they spot Thomas and the sleepers on the monitors. Sterling asks if there is a lockdown, and Bell suggests that they use Sterling’s security access to activate the lockdown. The corporal warns that there’ll be no escape from them, and Sterling admits that he knows.
As Thomas speaks to the detainees, Maya slips in with the crowd. Thomas finally asks the detainees to choose, and most of them go with him. A few of them, led by the Elder, prefer to remain in prison and hope that Sophia knows what she’s doing. Maya tells them that they should play along like she is, but the elder refuses. As the detainees head for the exit, Thomas sees Maya and compliments her on making the right choice. The sleepers prepare to leave, but Sterling activates the code, sealing the doors. Thomas sends his men to capture Sterling and force him to open the doors. Sterling and Bell realize the sleepers are on the way and head for the armory, and discover the Elder and his supporters, murdered. They talk to the dying elder, who confirms that Thomas had his men shoot them down. Presented with graphic evidence of Maya’s claims, Sterling considers the fact that Thomas’ plans are different from Sophia’s. Before they can move on, the sleepers capture them.
Senator Lewis prepares to go on Hardball With Chris Matthews
. Chris Matthews introduces her and Lewis tells the audience that she is going to pursue her husband’s goal of transparency, and that Inostranka is a violation of what he believed in. Martinez and Chief of Star Peel see the broadcast and try to reach Lewis and the studio staff to stop the broadcast. Martinez finally reaches Lewis by phone and asks what she’s doing, and she demands to know what Martinez is hiding. She promises to stop the interview if he tells her the truth, and Martinez stalls for time by saying that her husband knew about Inostranka’s true purpose and supported it. Lewis doesn’t believe it, and Martinez agrees to tell her the whole truth later. The senator accepts his offer and goes on the air to downplay her accusations.
As Michael tucks Samantha in, Leila tells Sean about her father’s ultimatum. Sean insists that her true origins don’t matter to him, but Leila points out that he hasn’t touched her since he found out. Sean takes her hand and apologizes, and Leila says that she has to go if she wants to get answers about her past. Sean tells her that she has to go and he understands, but Leila says that she can’t decide.
Thomas informs Sterling that he’s taking the detainees out and tortures him for the failsafe code. Outside, Maya secretly watches them as Sterling asks Thomas about the Elder and the other dead detainees. Thomas refuses to answer and prepares to shoot the director, and Bell finally gives in and gives them the code. Thomas frees the two prisoners and goes outside with his people. They handcuff Bell to a stanchion, and take Sterling with them. Maya blends in with the other escaping detainees, boards the helicopter, and sits next to Sterling. She then frees him and tells the director stop Thomas, insisting that not all of the extraterrestrials are on Thomas’ side. Sterling runs past the guards and tries to escape, but Thomas shoots him in the leg. Maya runs out to help Sterling and Thomas shoots her in the back. The alien leader prepares to dispose of her, but Aaron warns that they’re out of time and have to leave before the next shift arrives. As the helicopter takes off, Sterling goes to Maya and tries to help her. Dying, she tells him to believe her.
Leila wakes up the next morning and discovers that Sean has gone.
Sean walks down the road.
The matron arrives at Dr. Dempsey’s office and tells him that Leila and Sean freed their test subjects. Dempsey contemplates a black slab of stone covered in drawings and symbols, with small stones in various positions. He picks up a position and explains that it represents Sean, and says that past, present, and future are starting to blur and he’ll soon meet Sean.