At a bio-containment facility, the Avias Flight 514 passengers suffer from an attack on their nervous systems and cognitive function. Dr. Block warns that if the passengers' health keeps declining at this rate, none of them will make it through the night. Thomas calls President Martinez and takes responsibility for the passengers' plight. Thomas tells Martinez to release the Inostranka detainees within two hours or the passengers will die. It's 1944 at the Brooks Mountain Range. Sophia commands Thomas to leave the site of the crash with Simon and the other able-bodied survivors. Soon after leaving, Thomas and Simon realize that humans aren't technologically advanced and that "flying back" might take years.
Sterling reminds Martinez that it's government policy not to negotiate with terrorists. Moreover, if Martinez releases the detainees, it will be perceived as weakness. What Thomas is doing is an act of war so unfortunately there will have to be casualties. Even if that means the Avias passengers will die. Meanwhile Simon calls Thomas and urges him to back down. It's not too late to hand over the antidote and figure out a peaceful resolution. Thomas ignores Simon's pleas and reminds him that they've waited 66 years for their freedom. Thomas argues that Martinez is a wimp; there's no reason to think he'll get in the way of the detainees' freedom.
At the Snyder police station, Leila phones Sean and her parents, but her calls go to voicemail. She makes small talk with Officer Nugent, complimenting him on the family photographs on his desk. Behind the scenes, Officer Nugent and Carter begin to wonder if Sean will call Leila back, but Vicky has faith that Sean will respond. It's five years earlier in California. A shadowy man orders Vicky and her team of operatives to enter a home and kill an entire family. Vicky discovers a baby inside; she lifts her gun, ready to pull the trigger whenâ�¦ We're back to the present. At a convenience store, Sean calls his friend Rick from a payphone and asks him to run a "locate" on Vicky's cell number. Sean purchases a phone charger and finally hears Leila's tearful messages.
Sean calls Leila and promises to get to the station within an hour. As soon as Leila hangs up, a screen saver appears on Officer Nugent's computer showing his family - with a different father! Leila realizes that Nugent's an impostor and unsuccessfully attempts to escape. At the bio-containment facility, the patients' are in a dire state. Martinez desperately needs the antidote but he can't risk freeing the detainees' when so much of their agenda seems unclear. Christina reminds him that he was moments away from releasing them before the plane disappeared, but Martinez counters that things aren't as simple anymore. Christina feels that with so many innocent peoples' lives at stake, it's best to do whatever Thomas says.
Thomas phones to tell Martinez to release the detainees, but this time Martinez has the ultimatum. If Thomas doesn't hand over the antidote, Sophia and the detainees die. It's 1945 in New Mexico. Simon scolds Thomas for disappearing for six months. Thomas claims he's looking into developing nuclear energy with the U.S. government in order to use it to get back home. Simon worries that humans will misuse nuclear energy but Thomas couldn't care less. We're back to the present. Sterling tells Martinez that as a safeguard, Inostranka was built with a system that could seal off the cells and pump in carbon monoxide. Now that the mass termination is a real possibility, the gravity of what Martinez is planning to do weighs on his conscience. Simon meets Thomas to relay Sophia's message. Thomas resists, saying Sophia and Martinez are both weak. Thomas reasons that he was made leader for a reason; he'll be taking his own orders from here on out. Simon accuses Thomas of sending his own people to their death and storms off.
Simon tells Sophia that if Thomas lets the passengers perish, the Inostranka detainees are as good as dead. Angered by Thomas' callousness towards the passengers, Sophia tells Simon to relay an order: Thomas must hand over the antidote immediately. Thomas' pride has gone too far and it's time for Sophia to take charge. Simon meets Thomas to relay Sophia's message. Thomas resists, saying Sophia and Martinez are both weak. Thomas reasons that he was made leader for a reason; he'll be taking his own orders from here on out. Simon accuses Thomas of sending his own people to their death and storms off.
At the Snyder station, Vicky and Carter tell Leila that Sean's as good as dead. Leila begs Vicky to stop taking orders; Sean's an innocent person. It's five years earlier in Colorado. Vicky tells her supervisor that she wasn't told there'd be a baby at the house they targeted. Vicky lies, claiming she killed everyone in the house including the infant. But when Vicky returns to her home, we see that the baby boy is alive and well. At the Snyder police station, Vicky and Carter spot Sean and Collier only a block away. Right before Sean and Collier enter the station, Sean gets a call from Rick who says that Vicky's there too! Sean and Collier realize it's a trap.
Sean calls Vicky and tells her he knows where her mother and son are hiding. If Vicky harms Leila, Sean will make sure that everyone finds out about her secret family. Clearly terrified, Vicky teams up with Sean and kills the other captors. Sean rescues Leila and races off with Collier at the wheel. Vicky phones someone and claims that Sean - backed by F.B.I. agents - managed to rescue Leila. Thomas calls Martinez with a counter offer: Thomas will hand over the antidote to the Center for Disease Control if Martinez releases Sophia. All Martinez has to do is put Sophia on the Red Line. Martinez agrees but makes sure Sterling puts a sensor on Sophia so the government can track her.
Martinez phones Sophia to tell her that he's setting her free. He hopes she'll reign in Thomas' volatile streak. Sophia hopes to do more: she wants to regain Martinez's trust. At the bio-containment facility, Dr. Block watches as Thomas' antidote revives the tortured passengers, including Michael Buchanan. Meanwhile, agents accompany Sophia to the Farragut North subway station before letting her board the Red Line - alone.
Christina tells Martinez that she heard about the deal - the antidote in exchange for Sophia. But Christina needs to know - if Martinez didn't get the antidote in time, was he really planning on killing the innocent Inostranka detainees? Martinez can't answer her question. Christina leaves, clearly wondering if Martinez's idealism is finally giving way to politics. Across town, Sophia sits on a subway train, finally free. But where is she going? And now that she's being tracked by Martinez, will she lead him straight to Thomas?