Sean and Vicky run out of the Ambassador Hotel as the Vice-President's Secret service agents give chase. The two fugitives split up and Sean steals a van. He drives around, picks up Vicky, and they make good their escape. They pull off later to change out of their party garb, and Vicky insists that she's fulfilled her end of the bargain and they're done. Sean tells her that she's done when he says they're done, and warns her that if she walks away then he'll expose her son. Vicky begs him to let her go, but Sean says that she'll be free when they find Dempsey in France.
The military moves in on the church where Sophia, Thomas, and the sleepers have gathered. Leila emerges from hiding and watches the soldiers assemble outside, and then turns and sees Sophia.
In Washington, Sterling coordinates the assault as Lee arrives. The director explains that they located Sophia in Los Angeles, and that the President has sent in the military to end it once and for all. Sterling says that Lee has proved himself and that he'll need the agent's expertise. They enter the command center, where Martinez is coordinating the evacuation of citizens in the neighborhood. General Armbruster assures the President that they have secured the church and there's no escape, and Martinez says that they're done cowering.
In the church, Sophia receives a call from Martinez, who calls upon her and her people to surrender peacefully. She refuses to let him lock them up again, and he tells her that they have 10 minutes. Any resistance, and he'll make her regret coming to Earth.
With seven minutes remaining, Armbruster warns that the chances are good that Thomas will shoot, but he'll take the majority of the casualties. Sterling advises a cautious approach so that they can take prisoners, and Lee agrees. Martinez refuse to accept their advice.
As Thomas arms his people, Sophia tells him to have his people at the portal get them out. He refuses, saying it would give her control. She asks for his trust, but Thomas says that they can't contact Gerard, and by the time he contacts them it will be too late. As Michael reports on the forces against them, Leila finds him and he draws her off to the side. She apologizes for being there and wonders what is going to happen, and her father admits that he doesn't know.
Sophia calls Lee, who warns that Martinez won't negotiate. She tells him that their planet is going to be destroyed, and they can't surrender with the fate of their world at stake. Meanwhile, Gerard calls and Thomas explains the situation. He says that they can't teleport 188 people out unless they load the new uranium rods, and that will take hours. Sophia asks him what he can teleport out. A recon team starts to drill in the windows and Thomas' people open fire, taking down one soldier.
Martinez orders the assault to begin, and Sophia calls to say that the shooting wasn't supposed to happen. She tells him not to send in his men, but he hangs up and gives the order for the soldiers to begin the assault. Sophia looks at her people and then tells them to tell Gerard to take it down.
In Washington, the command center rumbles and Martinez realizes that Sophia is launching a strike of her own. Nearby, the Washington Monument collapses. The rumbling stops and Sterling gets a report of what has happened and tells Martinez the news. Martinez orders the soldiers to stand down before Sophia goes even further.
Martinez and his staff return to the command center and view the news broadcasts about the destruction. The President orders his staff to evacuate his wife and son, but refuses to leave. He then starts to dictate a speech about an attack by a terrorist group, but Sophia calls and asks for three buses and a cargo jet. If he doesn't grant her demands in one hour, she'll destroy Washington.
Sean and Vicky fly to France in a private jet that Vicky has procured via some favors. She asks him to let her talk to his son Adam and he sets up a link. Vicky talks to her mother, who says that Adam is asleep. Mrs. Larson tells them about the destruction of the Washington Monument, and asks Vicky to come home. After she cuts the connection, Sean checks the files and learns that Dempsey sponsors the Phoenix Foundation, and they have an archaeological dig in the Jura Mountains. He figures that Dempsey is looking for something and it's worth a fortune.
In France, Dempsey arrives and meets with the head archaeologist, Dr. Ellis. He shows his superior a dozen amphorae dating back two thousand years, but Dempsey says that they're far older. Ellis explains that one of them is inscribed with an unknown language. The chamber they removed them from has additional pictographs, but Dempsey angrily notes that no one was supposed to breach the entrance. Ellis assures him that he was the only one who entered the chamber, and Dempsey takes out a gun and shoots him dead.
In Los Angeles, Thomas notes to Sophia how hard it must have been for her, but she tells him not to try and pretend to understand her. She warns him that he eliminated diplomacy as a possibility, and Thomas insists that humans have always been hostile and self-centered throughout history. He admits he's made some mistakes but has united their people, but Sophia says he's only united them in fear. Thomas warns her that change isn't easy, and she says that leadership is never supposed to be easy. Sophia hugs him while Isabel looks on.
In Washington, Sterling asks to talk to Martinez alone. As he goes, Martinez tells his staff to give Sophia the busses because it's their only option. Outside, Sterling suggests that they have another option. He explains that he saw Thomas at Bethesda Hospital when Lee was recovering there. According to the footage, Thomas posed as a technician in the lab and switched Lee's DNA. They've been monitoring Lee's phone and determined that he's been making encrypted codes, and Sterling hopes to decipher them and finally get ahead of Sophia and the others.
Lee calls Sophia and objects to her actions, saying that she's turned away from their peaceful mission. Meanwhile, Sterling's technicians work to decipher the encrypted signal. On the phone, Sophia explains to Lee that they used up all of their fuel and right now she's bluffing.
In France, Vicky and Sean drive toward a safe house. He enters the code to keep her son's location from going out on the Internet, and then asks her for her contact's name. She explains that she knows the man as Henri, and that they worked together from time to time. Vicky refuses to tell him more, saying that it makes her vulnerable. They arrive at a villa and Vicky leaves Sean at the front gate while she goes around to the back. Henri captures Sean at gunpoint and prepares to shoot him, but Vicky arrives just in time.
Inside, Henry makes them a meal and talks about his past adventures with Vicky when she was a CIA agent. As Vicky goes to get some more wine, Henri explains that Vicky's CIA superior burned her to cover up his mistake and almost got her killed. He then asks Sean why Vicky is helping her, and Sean explains that he's blackmailing her. Henri admires him for that, but points out that Vicky doesn't do anything she doesn't want to do.
At the church, Michael comes to find Leila and tell her that they're getting out. She asks if they destroyed the monument and killed thousands, and wonders how her father could do it. Michael insists they had no choice, and Martinez would have locked them all up along with Leila. She insists that she isn't one of them, but Michael warns that Martinez won't make that distinction. He says that the humans are the monsters, and they'll always hunt them.
Dempsey and a lieutenant go to the chamber and examine the pictograms. They show guardian angels, and Dempsey explains that they are real creatures rather than metaphors. As he places his hand to the wall, Dempsey notices a triangular symbol. It matches a tattoo on his own wrist.
The three buses arrive at the church. Inside, Sophia speaks to her people and tells them to remain calm and controlled. She tells them to ignore the soldiers' guns and ignorance, and a new day is upon them. As the sleepers go to the buses, Isabel tells Thomas that he should be leading their people rather than Sophia, but he tells her that there are no sides anymore and orders her on the bus. Leila boards one of the other buses.
In Washington, the technician manages to decrypt the call between Lee and Sophia.
The buses leave for the airport, passing by the soldiers. Thomas confirms there's no pursuit to the rear.
The technician decrypts Sophia's statement that they're bluffing. Martinez orders his soldiers to take them out. Sterling objects, warning that the person with the portal is still out there and could launch more attacks. Martinez says that he's tried restraint but now they have to eliminate the threat by any means necessary.
An Apache helicopter closes in on the buses. Sophia and her people on the second bus spot the helicopter and she realizes that Martinez knows she's bluffing. The helicopter opens fire and blasts apart the lead bus. Thomas calls Gerard from the third bus and he confirms they have enough fuel to teleport one bus. Sophia calls to tell Thomas they have to surrender, but he tells her that she's the best chance to save their people. He explains that he'll run interference while Gerard sets the portal.
Martinez gets word that Sophia is on the second bus and tells his people to open fire.
Thomas has his driver pull his bus ahead of Sophia's. Sophia stares in horror as the missile strikes the bus, killing Thomas and the others. A portal opens on the road ahead and Sophia's bus enters it, disappearing.