After ratifying Jarvis as President, the cabinet gathers in the Oval Office to watch the Chief Justice swear him in.
The medics get Martinez to the OR and have Christina wait outside.
Sterling watches as Jarvis swears to execute the duties of the office of President of the United States.
Christina watches from outside the OR as the doctors attempt to relieve the internal pressure. However, they discover that there is no fluid causing the apparent pressure. Martinez flatlines and they manage to bring him back. However, he's in a coma
Simon is strapped to the bed at the gated community and watching the broadcast about the President's hospitalization. When Carlos comes in to give him some food and water, Simon warns him that Sophia has changed, and taunts him into coming closer. He then tries to grab Carlos and almost succeeds in freeing himself, but Carlos knocks him back, holds him at gunpoint, and warns Simon that humanity is doomed and Sophia is calling the shots at the White House.
Jarvis meets in the briefing room and starts by acknowledging Martinez's contributions. He then says that Sophia's people are undefeatable given their levels of technology, and he plans to open diplomatic channels. Jarvis orders a halt to all intelligence and military operations. When Sterling objections, saying they don't know what she is planning, Jarvis points out that their ignorance is Sterling's fault and says that they'll work out a way to live in peace.
Afterward, Sterling tells Peel that he got a sample of the spilled coffee from his cuff and has sent it to the lab for analysis. Until then, Peel warns that they'll have to stand down against Sophia and her people.
Carlos reports what happened to Sophia, and she receives a call from Evan in Murmansk. He tells her that the body they excavated has the Spanish Flu strain, but the men they hired were exposed and died on the ship. He tells her that their courier, Alex, is heading to New York by plane and has the lungs in a carrier suitcase.
At the airport, a blonde-haired man picks up his ticket and boards with the case. Sean and Vicky arrive at the airport seconds later and try to get the clerk to tell them if Alex got on the plane. She refuses to reveal the information, so Sean asks if they have tickets. While the woman checks, Vicky warns that she doesn't want to be on the plane with a potential WMD. Sean says he'll do it himself if he has to, and Vicky gives in and agrees to go with him. The two of them board just in time.
The plane heads for New York and Vicky goes to the rear stewardess compartment. Once she's alone, she steals the passenger manifest and rejoins Sean. There is no one named Alex on board, but Sean points out the blonde-haired man, who has been acting nervous. Their suspect returns to his seat, and Sean notes that he took his carryon with him to the bathroom.
Sterling goes to see Martinez, and Christina warns that his condition isn't good. She blames herself, but Sterling says that there's nothing she could have done. Christina realizes that he's hinting at something, but Sterling refuses to confirm anything further.
Dr. Lu reports to Sophia that Martinez will be dead in a day or so. Michael arrives in response to Sophia's summons, and she tells him that she's had trouble sacrificing her principles. Now she needs to eliminate Simon rather than risk him escaping and turn in them over to the authorities. When Michael asks why she's chosen him, Sophia says that he's never let his family attachments get in the way of what needs to do. After a moment, Michael agrees to her request.
Vicky walks past their suspect and spills her drink on him. He gets up, takes the case, and goes to the bathroom. Sean is waiting for him and manages to subdue the man as Vicky comes back. However, the lung samples aren't in the case, and they realize that he's smuggling coke. The male stewardess comes back and they assure him that everything's fine.
Back in their seats, Sean says that they have to let the authorities know there is a WMD on the flight. He wants Vicky to use his contacts in the CIA, but she warns that Alex could release the virus and kill them all. He insists that it's worth the risk as long as they contain the virus, and Vicky reluctantly gives him the name of her contact. As he works, Sean says that he's finally realized that she's helping because of her feelings for him, and is surprised given how they first met, as target and killer. Vicky takes offense and says that he's only a means to an end and she's doing it to protect her family.
Michael returns to his home and Leila informs him that she's buried Luis. As Michael prepares to leave, Leila asks how many innocent people are going to suffer. He insists that he doesn't like it but it's the sleepers or the humans. Leila talks about how when she was a child, she found a dead bird and Michael told her it was their responsibility as the strongest, smartest people on the planet to protect other life. She says that she looks at Michael and doesn't recognize him anymore.
Dr. Narducci reports to Sterling that he found traces of an unknown synthesized biocatalyst in the sweetener, and humans don't have the science to create it. Sterling goes to see Jarvis and tells him that he had the coffee tested and the lab found an unknown compound, and one he believes came from Sophia's people. He accuses Jarvis of working with Sophia and warns him that she's lying. Sterling begs Jarvis to put an end to it before it's too late. Jarvis denies the accusation and tells Sterling to tender his resignation, and the director turns and walks away.
Sean and Vicky watch as two F-16 jet fighters pull up beside the plane and redirect it to Andrews Air Force Base. They figure that Alex will make a move. One man gets up and heads for the front of the plane, but then says that he just wants to be seated by his wife up front.
Aaron calls Sophia to tell her that the plane has been intercepted. He suggests releasing the virus, but Sophia warns that it is too lethal to spread before the passengers die, and then gets another idea.
Jarvis meets with Peel and claims that Sterling buckled under the pressure. He suggests that Peel come to him if he has any concerns, but is interrupted when the phone rings. After Peel leaves, Jarvis takes the call from Sophia and she tells him to release the fighters escorting the plane. When he asks what the circumstances are, Sophia tells him to look out the window at what's left of the Washington Monument. If he refuses, she'll reveal his involvement to the world.
The F-16s retreat and Vicky warns that Sophia must have someone on the inside. The plane lands at JFK International and they overhear one of the flight attendants refer to the female attendant as Alexandra. They realize that she's the courier, but are caught in Customs while Alexandra walks out of the airport.
Jarvis receives word that Sterling has been escorted out of the White House.
Michael comes to see Simon and dismisses Carlos. He then aims his gun at Simon and fires... into the wall. Michael knocks out Carlos and tells Simon to get Leila and meet him outside the community, while he goes to get the poison antidote from Lu.
Once they clear Customs, Sean and Vicky spot Alexandra heading for the parking lot. As they approach her, a van cuts them off. There's a struggle and one sleeper takes down Sean. Vicky manages to disarm him and grabs his gun, but the sleeper grabs another gun and threatens to shoot Sean. Sean tells her to take the shot, but after a few moments she puts down the gun and kicks it away. The sleeper gets in a car with Alexandra and drives away. Sean asks why Vicky didn't take the shot, but she doesn't have an explanation. They steal a car and drive off after Alexandra.
Aaron goes to the infirmary and finds Carlos bound and gagged. He orders his men to lock down the perimeter. Meanwhile, Simon leads Leila through the woods but there's no sign of Michael. As the sleepers call in, Michael finally arrives and embraces Leila. The three fugitives head for the perimeter fence but Michael is shot and wounded. He gives the vial to Leila, who gives it to Simon and stays by her father's side. As Michael dies, Sophia and the others arrive and pull Leila away.