Sean drives a police car to a remote hotel parking lot. He enters a room carrying a bag full of medical supplies. Inside, Agent Collier lays on a bed, barely conscious and bleeding from her chest. It's two hours earlier. Agent Hobbes, Agent Collier and Sean encounter a police officer who's blocked off the highway due to a chemical spill. Sean insists the cop is lying, but the agents disregard him and turn the car around. Just then a car smashes into the FBI car, rendering everyone unconscious except Sean and an injured Collier. Sean frees himself from his handcuffs and pulls Collier from the wreckage just before the car explodes. Together, they drive the police car to safety.
Back at the hotel, Collier awakens handcuffed to the bed. She warns Sean that he's kidnapping a federal agent. Sean asks Collier to use her laptop to help him track down Vicky Roberts, but Collier says that can't be done wirelessly; she'd need to use a secure hard line at the Yuma FBI office. Discouraged, Sean pretends to take a shower while Collier phones for help. Sean stands behind the door, eavesdropping. Vice President Jarvis confronts Director Sterling about the investigation into the assassination attempt. Jarvis reminds Sterling that only a handful of people knew about the President's press conference; therefore, the suspect list should be small. Sterling says the investigation is ongoing, but a dissatisfied Jarvis pointedly asks, "Who investigates the investigator?"
In the Arizona desert, President Martinez sees the dead passengers of Flight 514. Sterling tells Martinez that since the passengers are dead, the official cover-up will be that the flight stopped transmitting flight data while flying over the Brazilian rain forest. Martinez objects to lying to the passengers' loved ones, but Sterling suggests it's the government's duty to protect the public from the truth. Simon explains that the passengers had defensive wounds and were clearly running from a singular threat. Sterling thinks the sleepers are behind this and tells Martinez that perhaps "more aggressive interrogation tactics" should be used on Sophia. Martinez disagrees, saying he has a plan.
Martinez confronts Sophia. He understands why she kept the sleepers' existence secret, but now 183 passengers are dead. Martinez needs to find out who was responsible. Sophia can only apologize and say it wasn't supposed to happen this way. She can't help Martinez find the sleepers because that would be a betrayal of her people. Martinez informs Sophia that he will release any Inostranka detainee who helps lead authorities to the sleepers. Sophia says no detainee would betray her people, but Martinez feels confident in his plan. At Inostranka, a detainee named William tells a guard that he's prepared to tell Martinez everything: how many sleepers exist, where they're hiding, and what they've been up to. All he wants is his freedom.
At the Pearblossom Inn, agents break into Collier's motel room and unshackle her. The bathroom window's open and there's no sign of Sean. Agent Spencer drives Collier down the stretch of highway near the car crash. Collier acknowledges that Sean could've run after the crash, but instead he came back to save her. Spencer wonders aloud about the cop's chemical spill story; after all, trucks aren't supposed to transport chemicals on Route 95. At FBI headquarters, Collier and Spencer investigate Sean. Meanwhile, in the parking lot, Sean sneaks out of Spencer's trunk carrying Collier's laptop!
Collier and Spencer see a breaking news report about Flight 514's disappearance en route to Sao Paulo. Collier realizes that Sean knew about the missing flight a full three hours before the it was reported missing! Meanwhile, Sean connects Collier's laptop to the FBI server and runs facial recognition on Vicky Roberts. Collier interrupts Sean's sleuthing and has him arrested. As Sean is escorted out, he shows Collier that Vicky Roberts has seven aliases. A police officer pulls over Vicky for a broken taillight. Leila is bound and gagged in the back of the van. When the cop asks Vicky to step out of the vehicle, she kills him.
In a hotel suite, Sterling asks William who was behind the plane's disappearance, how they did it, and where they are. William will talk, but first he wants money, protection, freedom, and his girlfriend Maya - an Inostranka detainee. It's November 2, 1944 at the site of the aircraft crash. An injured William wants to flee with Thomas, but Sophia says she can't risk anything slowing Thomas down. Seeing William's injury, Maya can't bring herself to abandon him. Back at the hotel suite, William promises to tell Sterling how to stop the sleepers before it's too late. But first Maya must be freed. Sterling gets Martinez's permission to give William whatever he wants.
Simon tells Sophia that William has agreed to talk as long as Maya is freed. Though Sophia is extremely concerned, she knows William hasn't revealed information yet. Simon asks how Sophia can be so sure. "Because we're still alive," she responds. Sophia cryptically states that she should have dealt with William when she had the chance. It's her responsibility to protect her people and perhaps she was too lenient. She tells Simon, "Now you'll have to deal with him. Harshly."
Sterling and his aide Justin listen to the mangled, partially destroyed black box recordings from Flight 514. They hear Sean Walker, a passenger who snuck onto the flight. According to his file, Sean's a bright kid, who at 16 hacked into a Pentagon server just for the fun of it. He graduated from MIT and freelances as a software programmer. Shockingly, the Yuma FBI has just arrested Sean. That makes him the sole survivor of Flight 514! At the FBI office, Collier and Spencer investigate Vicky Roberts' many identities. Though they can't prove anything, Vicky seems to be some sort of underground government operative. U.S. Marshals arrive for Sean Walker, but Collier suspects something's off. When she tries to make a call to verify Sean's transfer, a shoot-out ensues!
Vicky drives her van into the Vokolov Shipping Company. Carter helps unload the body of the slain police officer while Vicky deposits Leila in a makeshift cell. In an attempt to escape, Leila stabs Vicky with the cop's badge but is unable to do any major damage. In spite of Vicky's bullying, Leila stays strong and insists that Sean will rescue her. Back at the FBI office, Sean and Collier have become an unlikely duo, desperately trying to kill the armed madmen disguised as U.S. Marshals. Sean and Collier manage to kill two of the three attackers and rush out of the office unharmed. Sean and Collier speed off as the third attacker fires at their vehicle.
Escorted by guards, Maya arrives at William's hotel suite. The reunion is tearful and moving until Maya asks how William arranged it. He explains that he promised to reveal information as long as Maya was released. Now that he knows the U.S. government is trustworthy, he plans on telling them whatever they want to know. William walks Maya to the window and shows her a taste of freedom in the form of the beautiful D.C. skyline. Clearly distraught, Maya gazes out the window before turning around and stabbing William. She apologizes and tells him to keep imagining his dream future.
Back at the Vokolov Shipping Company, Vicky has a gun to Leila's head when suddenly Vicky's cell rings. It's Lonner, the third and only surviving gunman from the Yuma FBI massacre. He tells Vicky that Sean's managed to escape with the help of an FBI agent. With Sean a free agent, Leila must remain alive. She could be an important gambling chip. "I told you he'd come back for me," Leila says. At a temporary morgue for the Flight 514 victims, a soldier hears what sounds like labored breathing. One by one, each of the passengers begins to breathe and sit up. They're alive!