The alien satellite explodes and pieces plummet back to Earth. Newscaster reports on the unscheduled missile launch but have nothing definite to say. All they do is pass on the government statement that it's a plane crash.
Martinez informs his staff, including his chief of staff Richard Peel, that he's been keeping secrets. He informs them that the extra-terrestrials have a number of sleeper agents among them, and they launched a communication satellite that released a seven-second burst into deep space before self-destructing. All intelligence agencies have been instructed to decrypt the signal. One technician comes up with a breakthrough and reports to Sterling. Sterling informs the president that they have the first line of the message: "Preparations are being made for your arrival."
Martinez meets with Sterling and Peel in the Oval Office. Sterling warns that they should expect an invasion, but Peel isn't convinced. The director warns that superior firepower will eventually win out, and the head of the Armed Forces warns that they have no idea where to strike. Sterling suggests that they interrogate the detainees now that they have a clearer picture of what's going on, and Martinez tells him to go to Inostranka and supervise it personally.
Sophia meets with Simon and warns that they don't know how many of their people Thomas plans on bring over. She tells Simon to go to the portal array, but he warns her that Thomas has kept it secret on the grounds of compartmentalizing the information. Simon suggests that there is one of their own who could help them stop Thomas. Sophia doesn't like it, given what Simon's proposed ally did to them, but Simon warns they don't have any other choice.
In the Himalayan Mountains, Thomas and Isabel meet with Gerard, one of their own. They show him the power module, and Gerard warns that he'll need more staff to make their plan a reality. Thomas assures him that they have a plan that will get more of their people. Gerard then takes them to see the portal array: a huge metallic superstructure almost a mile in diameter. Thomas is confident it is large enough to bring every last one of their people there.
At the Willowbrook Hospital in Missouri, Sean and Leila go through the charred files and Sean finds the file with Michael Buchanan's name on it. It shows that he has been around for decades, unaging, and Sean wonders if Michael is one of them. Leila insists that there isn't any "them" and the photos are fakes. She wants to talk to her dad and find Samantha, and begins searching desperately through the remaining papers. Sean hears a noise outside the room and they go to investigate. They spot the matron, who flees up the stairs. Sean easily captures her and draws a gun on her, and demands answers. Leila examines her briefcase and finds vials of liquid. The matron tells them that all of the test subjects have been moved, and that they take Samantha and the other girls because they're special. She says that Leila is special because of her father, who doesn't age at a normal rate. Leila demands to know where Samantha is, and Sam threatens to shoot her. The matron explains that Samantha is being sent to a facility at West Plains with other girls, and left in a white van ten minutes ago.
Leila and Sean leave the matron behind and drive toward West Plains. She asks him if he believes what the matron said about Michael, and Sean notes that everything they've heard has been proven true despite how strange they sound. Leila says that she knows.
At the CDC facility, Michael is transferred to a supermax facility in Virginia. En route, a car crashes into the transport van and masked men quickly subdue the soldiers and free Michael. They throw him into the van and one of them removes their mask. Michael realizes that it's Simon.
Peel informs Martinez that the news story on the missile has been covered up, Sterling is en route to Inostranka, and Martinez is to meet with Senator Catherine Lewis of Alaska, who has taken over her dead husband Bernard's seat. Martinez meets with her and Lewis explains about the bill she's supporting on fiscal responsibility. He agrees with her and promises his support, and Lewis insists that she wants transparency in government. Lewis then explains that she's found a file in her husband's briefcase about a weather station at Inostranka. It has financing information on the "weather station," but she was told it was never built. Martinez hastily lies that the project never came to fruition, and promises to get her information on it. Once she leaves, Lewis confirms with her aide, Eric Watkins, that he kept a copy of the file and that she believes that Martinez was bluffing.
Simon brings Michael to Sophia, and Michael asks for her forgiveness for flying the plane. He explains that he didn't know she would be there at the Presidential compound, but admits that he would have gone through with it anyway because their enemies had his daughters. Sophia points out that he wasn't supposed to have daughters, and snaps at him for spending time building a family while she sat in prison for decades. She then confirms that Michael helped Thomas transport the portal components via a middleman, and wants the identity of the middleman so they can find Thomas. Michael agrees to help, but first asks her to help him locate Leila and Samantha. He figures the government knows something, but Simon says that all they know is that Sean has surfaced from time to time. He starts to offer his help, but Sophia says that Michael will obey her. Michael refuses to back down and tells her that his help is conditional on her help finding his daughters.
In the white van, Samantha and the other aged girls wait to arrive at their destination. Behind them, Sean and Leila catch up and close in on the vehicle. Sean passes the van and confirms that the driver is alone, and then pulls ahead. The van driver tries to ram them off the road, and Sean brakes. The van goes off the road and slams into some rocks. Sean and Leila approach the van and Sean knocks out the driver and gets the keys. They free Sam and the other girls, and Sean and Leila get Sam out and tell a passing driver to call for help for the other girls. When their car won't start back up, Sean and Leila flee into the woods with Sam.
At a bar in Alaska, Isabel buys a drink for a soldier, Lieutenant Grier, and he joins her. As they leave, he asks about her leg and she claims it was hurt in a skiing accident. Thomas grabs Grier and tells him that his family is hostage, and they want him to help raise an army.
Samantha finally tires out, and asks why they're running from the police. Leila explains that they want her to be safe. Collier calls Sean and tells him that she's sending Federal agents to lock down the scene. She also informs Sean that someone called for Michael and wants to set up a meeting. Sean figures that it's a trap, but Michael sent a message to confirm the truth: that he knows Sean was going to propose to Leila on the cruise. Collier texts him the number and Sean tells Leila about the proposed meeting.
In Washington, Lewis arrives at her office and finds Niles Duncan, the sergeant at arms, securing her husband's office. He explains that he's been ordered by the President to confirm that the files don't contain any classified information. Lewis claims that there are letters in her husband's death that were sent to him by another woman, and asks to retrieve them in return for owing him. Niles agrees and clears his men out. Once she's alone, Lewis pulls the files on Inostranka.
At Inostranka, Major Pearson greets Sterling, who says that he plans to interrogate the detainees and that Pearson doesn't have the clearance to receive further information. Meanwhile, Grier is working in the command center.
Sean, Leila, and Sam wait to meet with Michael. Leila asks Sean what it means if Michael is one of the aliens, and what it makes her. Sean assures her that everything will be all right. Michael arrives and Leila and Sam run to hug him. Simon is with Michael and thanks Sean for what he's done. Leila backs away from Michael and says that Madeline told them about the aliens, and that they found the photos of Michael. She asks her father if it's true, and he admits it is as he hugs her and apologizes.
At Inostranka, Thomas and his troops cut their way through the perimeter fence. The soldiers easily get inside and take out the guards. They then let in the rest of Thomas' men.
Corporal Bell escorts Sterling to see a detainee, who explains that the interrogation subject murdered a suspect on Sophia's orders and he wants to know why. He enters the room and greets Maya, and tells her that they've deciphered the message from the satellite. Maya says that invasion would violate the precepts of her people, and that they swore an oath to protect humanity. She explains that they vowed to leave Earth's civilization intact, and Sterling asks her what the message means.
Thomas' men drive in and claim they're on a supply run from Fort Greely. The guards call Grier to confirm the supply run, and he tells them to permit entry. Grier then inserts a flash drive into the computer and blanks out the security monitors. Pearson comes in and notes that Grier is looking ill, and the lieutenant quickly makes an excuse.
Once inside, Thomas' soldiers gas the soldiers on duty. As they spread out, Thomas tells them to keep quiet until they secure the facility.
In the command center, Pearson notices a clock on the monitor that doesn't show the correct tape. He checks the other monitors and realizes they're on a loop. Grier draws a gun on him before Pearson can give the alert. Thomas storms in and says he wants the prison and everyone in it.