The Chief Justice swears in Jarvis as President. Meanwhile Martinez seizures, bringing him closer and closer to death! Moments later he lapses into a coma.
At the Sleeper community, Simon sees news of Martinez's troubles and immediately knows Sophia is somehow behind it. When Simon voices his disappointment to Carlos, their heated conversation turns into a physical altercation. Carlos pulls a gun on Simon and tells him to accept the inevitable: the native population doesn't have a chance. Sophia's calling the shots from the White House now. Simon realizes just how powerful Sophia has become.
At a private White House meeting, Jarvis urges his staff to open diplomatic channels with Sophia and her people. After all, they have unbridled power so there's no point in acting in a belligerent fashion. Later, Sterling and Peel complain about Jarvis' new approach. Sterling tells Peel that some of Elias' coffee spilled on his shirtsleeve. It's currently being analyzed for traces of poison. At the Sleeper community, Sophia phones Aaron who says the dead body they excavated is still rife with the strain of the virus. Aaron mentions that it might kill too quickly; when the men who operated on the body were exposed to it, they died instantly.
Aaron tells Vicky that the virus is en route to America on a plane from Russia. Alex, the courier, will make sure it arrives on schedule. Sean and Vicky board the same plane looking for the mysterious shipment. Vicky searches the list of passengers but doesn't see one named Alex. Sean notices a suspicious man carrying a briefcase. Could he be carrying the malevolent strain? Christina tells Sterling that she feels somehow responsible for Martinez's failing health. Sterling assures her this is not her fault but doesn't explain any further.
Dr. Lu tells Sophia that Martinez will die shortly. Dr. Lu exits and Michael meets with Sophia. She tells Michael that her actions have taken a toll on her. It's been very difficult continuing in Thomas' absence. Then Sophia tells Michael that he must kill Simon. After all, Simon attacked Carlos and seems hell-bent on escaping. Sophia says Michael has proven his loyalty and must put this plan into action. Back on the flight, Sean and Vicky attack the suspicious passenger and open his briefcase. Inside, they find coke, not the infected lungs they were searching for.
Sean suggests that he and Vicky alert someone that a W.M.D. is on board. Vicky rejects the idea, saying the courier might panic and unleash the virus on the passengers. Besides, why would anyone believe them? Finally Vicky gives in and tells Sean she knows someone at Homeland Security. Sean thanks Vicky for helping and adds that sometimes it's hard to believe that a trained killer such as herself would help him in his cause. Offended, Vicky says she's on this mission for herself and her family, not Sean.
At the Sleeper community, Leila tells Michael she's found a remote spot where they can bury Luis. Then Leila asks Michael when he feels Sophia will stop her devious actions. How many will have to die? Michael defends Sophia, saying, "It's us or them." Leila vocalizes her disappointment saying her father taught her to defend and protect the weakest among them. The criticism resonates with her father. A forensic analyst tells Sterling that he found an unknown biocatalyst in the coffee stain on Sterling's shirt. It possessed something synthetic that humans couldn't have created.
Sterling accuses Jarvis of working with Sophia in order to poison Martinez. Sterling tells Jarvis that some of the poisoned coffee spilled on Sterling's shirt; this sample possessed an "unknown compound" - clearly a poison created by Sophia's people. Sterling tells Jarvis that he's a pawn in Sophia's game. Enraged, Jarvis fires Sterling.
Sean looks out the window to see an F-16 flying next to the commercial jet. A flight attendant tells the passengers that they are under military escort and have been redirected to Maryland. Clearly, Vicky's contact was very powerful. Aaron phones Sophia to tell her that the flight has been redirected; someone must have found out there was a W.M.D. on board. Aaron suggests they tell the courier to unleash the virus on the passengers, but she says the virus kills too quickly. The passengers would all die before it spread properly.
Jarvis meets with Peel to tell him of Sterling's firing. Jarvis further explains that Sterling made preposterous allegations that he trusts nobody sane would believe. Moments later, Sophia phones Jarvis to tell him that U.S fighter jets are currently escorting a commercial jet away from New York, the intended destination. Sophia tells Jarvis to release the hold on the plane so it can continue on its proper course. When Jarvis asks for more information, Sophia warns him that he better follow orders or she'll kill more innocent people and tell the world what Jarvis did to Martinez. Jarvis finally realizes what Sterling said is true: Jarvis really is Sophia's pawn.
The captain tells the flight that the security threats were determined to be non-credible and that the flight will no longer be diverted. The F-16s fly away, leaving Sean and Vicky fearful. Later, the plane lands and Vicky and Sean notice one flight attendant is named Alexandra. She must be the "Alex" who is carrying the virus! Trapped in customs, Sean and Vicky can only watch as Alex gets away!
Sean and Vicky tackle Alexandra in the parking lot and try to wrestle her suitcase away from her. An armed man grabs Sean and puts a gun to his head. Vicky can't bear to see Sean killed so she allows Alexandra and her henchman to flee. Instead of killing Simon, Michael makes the shocking decision to set him free! Michael, Simon and Leila attempt to make a run for it. Just before they escape, a Sleeper shoots Michael to death! Before he dies, Michael gives Simon a vial containing the antidote for Martinez's illness. Simon flees while Leila holds her dying father.