The President’s cabinet gathers in the Oval Office to witness Jarvis being sworn in as the President of the United States.
At the hospital, doctors try to revive Martinez, who has seized. They get him to the OR, ask Christina to stay outside, and get him onto the operating table so they can relieve the pressure on his brain.
Sterling watches as the Chief Justice swears in Jarvis.
The doctors save Martinez, but the President goes into a coma.
At the gated community, Simon is strapped to a bed and watching the broadcast of the President’s hospitalization. Carlos comes in with some food and water, and Simon warns him that Sophia is committing genocide and violating all of their principles. When Carlos comes closer as Simon taunts him, the prisoner manages to grab him with legs. After a struggle, Carlos manages to break free and tells Simon that Sophia has her agent in the White House now and there’s nothing that humanity can do to stop the sleepers.
Jarvis starts by calling the cabinet and advisors into the briefing room, and saying a few words in honor of Martinez. He then declares that they have no choice of defeating Sophia and her people given their superior technology, and he plans to open diplomatic channels and negotiate a peaceful resolution. In the meantime, Jarvis orders them to cease all intelligence and military operations. Sterling objects, warning they don’t know what the sleepers are up to, and Jarvis notes that it’s Sterling’s fault for failing to provide them with sufficient intel, and that they have no choice but to try and coexist.
After the meeting, Sterling tells Peel about the coffee stain that he found on his cuff, and that he has sent it to the lab for analysis. In the meantime, Peel warns Sterling that he’ll have to obey Jarvis’ orders and cease operations against the sleepers.
Carlos reports Simon’s attack to Sophia, and as they talk she receives a report from Evan in Murmansk. He updates her on the shipping of the lungs infected with the Spanish Flu from Murmansk to the U.S., and that they lost the hired mercenaries and doctor on the freighter. Evan concludes by telling her that the courier, Alex, is on their way.
At the airport, the last few passengers board the plane. Sean and Vicky arrive at the counter and try to find out if an Alex is on the plane. The flight counter attendant refuses to give out the name and Sean asks her to check if there are any remaining seats. As she does, Vicky admits that she’s reluctant to get on a plane with a WMD, and Sean says that he’ll go with or without her. She finally agrees to go and they buy the last tickets on to the plane.
As the plane takes off, Vicky goes to the rear compartment and steals the passenger manifest, and then rejoins Sean in their seats. None of the passengers are named Alex, but Sean notices a nervous-looking blonde man who has taken his carry-on case with him to the restroom.
Sterling visits Martinez at the hospital, and Christina informs him that her husband is in a coma and the doctors aren’t confident of his chances of success. She blames herself and Sterling suggests that she couldn’t do anything. Christina realizes that he’s referring to someone else being responsible, but Sterling refuses to say anything further.
Sophia receives a report from Dr. Lu that Martinez will die from the position within the next day or so. Michael arrives and Sophia admits that she’s concerned by the fact she’s had to go back on her principles. She tells Michael that they need to eliminate Simon rather than take the chance of him escaping and going to the authorities, and asks Michael to eliminate him. When Michael asks why, Sophia explains that he has always done what he had to regardless of his family attachments. Michael considers her request and then agrees.
On the airplane, Vicky spills her drink on the blonde man as she walks past him. When he goes back to the restroom, Sean ambushes him and they struggle. Vicky arrives and helps him, and they discover that the case holds cocaine rather than the lungs. A male stewardess comes back and they let the courier go, and assure the stewardess that everything is fine.
Back in their seats, Sean insists that they notify the authorities that there is a WMD on the flight, and that Vicky should contact one of her former contacts in the CIA. She worries that Alex could release the virus and kill them all. Sean is willing to do so if it means saving the world, and Vicky reluctantly gives up the name of her contact. As he sends the e-mail, Sean thanks Vicky and admits that he’s finally realized that she’s helping him because of her feelings for him. He admits that he’s surprised given that originally she was sent to kill him. Vicky takes offense at his insinuation and says that she doesn’t care for him, and that she’s only helping him to protect her family.
Michael returns home as Leila returns from burying Luis in the woods. He prepares to leave but Leila asks how many people will die because of what he’s willing to do. Michael insists that it’s them or the human, but Leila reminds him of when as a child, he told her that they had to protect lesser species. His daughter tells him that he’s not that man anymore.
Dr. Narducci arrives to inform Sterling that he found traces of an unidentified synthetic biocatalyst in the coffee, a biocatalyst beyond human technology. Sterling then goes to see Jarvis and tells him what he’s discovered, and that he believes Sophia’s people are responsible. He then accuses Jarvis of working with them and asks him to reconsider before it’s too late. Jarvis denies it and tells Sterling to tender his resignation. Sterling pauses and then leaves.
Two F-16 fighters arrive to escort the passenger plane to Andrews Air force Base. Sean and Vicky realize that Alex will have to make his move. One man gets up but only to sit with his wife further forward in the cabin.
Sophia’s lieutenant, Aaron, receives word of the fighters and calls Sophia. He suggests that they release the WMD on the plane, but Sophia notes that they now know that it incubates too rapidly for the passengers to survive to carry it off the plane. She tells Aaron that she has another idea.
Jarvis calls Peel into the Oval Office and claims that Sterling cracked under the pressure, and that the Chief of Staff come to him if he has any concerns. As Peel leaves, Sophia calls Jarvis and tells him to order the F-16s to stand down. He demands a reason but Sophia reminds him that they already took out the Washington Monument, and will cause more devastation if he balks. Finally, Sophia warns that if he doesn’t follow her orders, she’ll reveal his involvement with her to the world.
The F-16s back off and Vicky realizes that Sophia must have somewhat on the inside who is highly placed in the government. The passenger plane lands at JFK International and as the passengers disembark, Sean and Vicky realize that one of the female attendants is named Alexandra. They realize that she’s the sleeper and try to follow her off the plane, but are held up at customs while the attendants continues through.
Jarvis receives word that Sterling has left the White House.
Michael dismisses Carlos and goes to talk to Simon. He shoots at him... and deliberately fires into the wall behind the former FBI agent. Michael then knocks out Carlos and tells Simon to get Leila and meet him on the perimeter after he gets the poison sample from Dr. Lu.
Sean and Vicky finally get through Customs and follow Alexandra to the parking garage. A sleeper driving a van cuts them off and attacks them. Vicky manages to disarm one of their opponents and grabs his gun, but another one holds Sean hostage. Sean tells Vicky to shoot, but she drops the gun and backs away. The sleepers escape with the case and Sean demands to know why Vicky didn’t shoot despite the threat to him. She doesn’t have an answer for him, and they steal a car to go after Alexandra and the case.
When Devon goes to the infirmary, he finds Carlos and frees him, and then orders the sleepers to lock down the perimeter. Simon gets Leila out to the woods where they meet Michael, who has the antidote. They head for the fence but Michael is shot and mortally wounded by the pursuing sleepers. As he lies on the ground, he gives Leila the vial. She gives it to Simon and tells him to take it to the authorities, as she plans to stay with the father. Simon leaves, and Michael begs his daughter to forgive him. Sophia and her people arrive to take Leila prisoner, pulling her away from her father’s corpse.