The passengers get out of the plane and Sean looks back... and sees Michael get out of the plane.
Four days earlier
Michael finds himself tied up in a locker room. A mercenary, Carter, comes in and Michael says he won't do it. Carter warns that Michael knows what they're capable of, and demands that he agree. When Michael refuses, Carter takes him to a peephole and shows him Leila in the next room, and Vicky pointing a gun at his daughter's head. Carter warns him that he'll have Leila shot and asks Michael for his answer again.
Sean asks Michael what happened, and Michael explains that his wife is dead and they were going to kill Leila, and that one of the women was Vicky. Sean realizes who it is. Helicopters arrive but Michael warns Sean that they can't trust anyone, and Sean is the only one who can help Leila. He tells his son-in-law to go and find her, and Sean reluctantly runs off into the desert.
In Florida, the Secret Service agents get the President and his family way from the retreat. Martinez. They go to the airport and fly Christina and David to the Presidential bunker. Martinez talks to Sterling, who has learned that the pilot, Michael Buchanan, hijacked the airplane to crash it into the compound. Martinez wants to know how the plane disappeared, and they go into the control room. The staff confirms that they have discredited all local witnesses and claimed the plane disappeared into a cloud layer. So far, the story is that Flight 514 is heading for Brazil. The Air Force determine that there's no sign of the plane, but they detected a massive blast of electromagnetic energy at the same time the plane went missing, and knocked out all the electronics at the site. However, they have no idea what it means. Martinez wonders if the military has a weapon that could account for the disappearance, but is informed that they do not. Sterling insists that only one other group could have engineered the plane's disappearance.
Thirteen months earlier
Martinez meets with Sterling and his people and demands a complete answer. The director explains that in 1944, an airplane of unknown origins crashed in the mountains in Alaska. The military locked down the scene and apprehended 97 survivors, many of them wounded. The survivors were identified as aliens. Sterling explains that Agent Lee oversees the facility, and Lee informs Martinez that the aliens look much like them. However, there are differences. They age at a much slower rate, but they only have a 1% variation in DNA. Sterling insists that it's a significant difference. Martinez wonders why they're holding them, and Sterling explains that the aliens have refused to explain why they're really there or what they want. He insists that they have a hidden agenda.
Sean makes his way across the desert but soon collapses from the heat.
Seven days earlier
On the cruise ship, Leila is sick the next day, she insists that Sean go snorkeling without her. He insists on staying and Leila thanks him for his thoughtfulness. Vicky arrives and tells them that Greg went on a jungle excursion. Leila tells Sean to go without her, and he reluctantly gives in. Vicky tells Leila to take care of herself and goes with Sean.
Once they're gone, there's a knock on the door. Leila answers it and finds Greg there. He says he came by to check on her, and she tires to usher him out. Instead he comes in and offers her a megadose of Vitamin C to get rid of her hangover. She passes and he tries to massage her foot. When Leila points out that Vicky might object, Greg says that Vicky and Sean are getting together. Leila goes out and finds a ship's officer outside: Carter, disguised. Carter tells Greg to leave, and when he refuses, stabs him in the chest. Leila runs out of the cabin but is captured by the security guard and drugged unconscious.
Sean wakes up at St. Francis Hospital and the nurse, Leanne Timmons, explains that a couple found him in the desert. She says that he was rambling about being in a plane crash, but that there's no report of a crash. Sean wonders where they are, and Leanne explains that they're in Yuma, Arizona. He asks to talk to the police, and the nurse dismisses it as symptoms of heat stroke. When he tries to explain that he was on a cruise, Sean realizes how insane it sounds, but insists on talking to the police.
Leanne calls for Sean and contacts Deputy Hode. When she identifies Sean, Hode says that he's wanted on a Federal murder warrant for Greg's death. Hode tells Leanne to keep Sean there until officers can arrive to arrest him.
Sterling warns Martinez that Sophia and her people are responsible, and that they have sleeper agents who made the plane disappear. Martinez demands to see Sophia, and is taken to where she's being held in a cell. Sterling insists that Sophia has been lying to them for six decades, but Martinez insists on seeing her.
November 2, 1944
In Alaska, a pilot flies over the crash site and spots the vessel. The arrivals are tending to each other and Sophia looks up to see the plane pass overhead. She calls out to Thomas and warns him that they'll be here soon. Thomas says they have to move everyone out, but Sophia warns that the wounded won't make it far. She tells Thomas to take those who can walk, while, she stays with the injured ones. Thomas wants to fight, but she tells him that they'll be together soon.
Martinez enters the cell and gives Sophia a chance to explain why she deceived him. All Sophia will tell him is that they mean him no harm, and her people saved his life. He wonders if her people were trying to save her, and wants to know here the plane can be found. Sophia says she can't tell him, and Martinez tells her that she's going back to Alaska with her people. Sophia says that it's a mistake and her people's patience is running out.
In Yuma, Leanne tells the staff to relax and then assures Sean that she called the police. As she changes his IV drip, he realizes that she's nervous about something. Once she leaves, Sean hears the police pulling up outside, along with FBI agent Collier and her partner. Sean goes to find Leanne, who begs him not to hurt her. She explains that Hode told her that he killed someone. Shocked, Sean tries to slip away but Leanne alerts the agents. Sean runs for it.
Five years earlier
Sean is at a swimming pool in Boston practicing for a meet. When he's done, he notices a girl, Leila, trying to learn how to swim. He goes over and they chat, and then he offers to help her learn. He holds her and helps position her head. Sean then offers to meet her there tomorrow for another lesson, and she immediately agrees
Sean runs past the deputies and ducks into a closet. Once the agents go by, Sean runs back and manages to get to the lobby... only to find the agents waiting for him. They arrest him for the murder of Greg Kervin.
Sterling goes to see Lee and tells him that Sophia's been lying, and he wants Lee to be part of a special operations team to find the aliens that escaped in 1944 and have been hiding plain sight ever since. The director worries that they have no idea how far they've been infiltrated.
Ten Years Earlier
At Langley, Virginia, a nurse takes a blood test from Lee, who explains he's hoping for field work in clandestine operations. She assures him that he's made it and welcomes him to the CIA. Afterward, Lee goes to the restroom and checks on a small incision further up on his arm. He then pulls out the implanted artificial vein that he used to fake the blood test.
Sterling tells Lee to find out every alien and do whatever he has to. Afterward, Lee goes to a deserted office and meets with Thomas. The two men embrace each other, and Lee warns that the prisoner exchange is now off the table. Thomas admits that their resources are drained and they should have let the military shoot down the plane. Lee insists it wasn't acceptable to him or her, and asks where the plane is. He notes that Thomas was supposed to set it down unharmed, and wonders why there is no word of the passengers. In response, Thomas says that the plane is in Arizona, and that he has plans for the passengers. As he leaves, he tells Lee that the agent will understand when he sees the plane.
As Collier and Www drive Sean away, he tries to explain what happened, but they don't believe him. He tells them that Vicky Roberts is involved and they need to find her. Collier points out that it would have taken a massive conspiracy to pull it all off, and that he suffers from narcissistic delusions. Sean recognizes the landscape from when he came in from the desert, and they find a deputy blocking off the road. Sean insists they crashed just over the rise. The deputy comes over and says that a semi jackknifed up ahead and they'll have to take a detour. Sean begs them to go through the roadblock. When they refuse, he begs them to find Leila, but Collier wonders if Leila even exists. Sean talks about how they were going to get married, but the agents ignore him and take the detour. They leave, unaware that the plane is just over the rise and government military vehicles are arriving. Lee and his men get out and examine the wreckage, and find Michael Buchanan, dead. Nearby are the corpses of all the passengers and crew of Flight 514.