Sophia and her people catch up to Leila and drag her away from Michael’s corpse, and the girl blames Sophia for his death. Dr. Lu arrives to inform Sophia that Michael took the counteragent to Martinez’s poison. They confirm that the counteragent isn’t on Michael’s body and that Simon must have taken it with him. Carlos suggests they send their people after Simon, but Sophia warns that the former agent is too experienced and that there is another way. She then orders to take Leila away and evacuate the compound.
At Martinez’ hospital room, Christina calls her to son to assure him that his father will be home soon. Dr. Reed warns her that they’ve done everything they can and Martinez is still dying, and Christina refuses to admit defeat.
Jarvis meets with Peel to choose a replacement for Sterling, and Peel insists that Sterling is still the best man for the job. The new President angrily warns that Peel might be seen as having sympathies toward Sterling, but then apologizes. As Peel leaves, Sophia calls Jarvis and tells him that Simon has the counteragent and if he gets it to Martinez, then Jarvis will lose everything he’s worked for. When he wonders what he can do, Sophia tells him to use all the powers of the U.S. government to find and eliminate Simon.
Sean and Vicky try to pick up Alexandra’s trail, as Sean taps into the GPS on the rental car the sleeper is using. Vicky suggests that they contact the police, but Sean reminds her that someone high up in the government called off the fighters.
At the new safehouse, Carlos tells Sophia that Gerard has received a report from their home world that things are worse than anticipated, and that radiation levels are quickly reaching lethal levels. Sophia then meets with Dr. Lu, who explains that the aliens are immune to the Spanish Flu, but it is too fatal in its current condition to make an effective bioweapons: anyone infected with it would die before they could contact others and spread the disease. Since the humans on the freighters died under confined conditions, it wasn’t an effective test of the virus in uncontrolled conditions. Sophia assures Lu that she has a plan underway for a more effective test.
Sterling is at home reading about Jarvis when he hears someone moving in the house. He draws a gun and approaches the intruder, and is surprised to discover that it’s Simon. Simon explains that he’s come to Sterling so that he can help Martinez, and insists that he wants peace between his people and the humans. He shows Sterling the counteragent and notes that Martinez is dying whether they use it on him or not. Sterling takes the counteragent and then looks outside and spots two Federal agents watching his house. He confirms that Simon wasn’t followed and concludes that Jarvis has put a tail on him following Sophia’s orders.
Simon’s former partner, Mike Garret, is in the car watching Sterling’s house. He spots Simon in the house and orders his men in.
Sean and Vicky track the rental car to a shopping mall. They approach the car and confirm that it’s empty, and then search it. There’s no sign of the case containing the lung samples inside, but there are blueprints of the mall’s air circulation system.
Alexandra tells her bodyguard, Roman to go to the security room and send all the video feeds to Sophia and Lu so they can watch how the infection spreads, and then meet her on the roof. She then goes to the roof and opens one of the specimen containers.
As Garret and his men surround Sterling’s house, the police pull up and order them to drop their weapons. Garret shows them his ID and an officer explains that they received a 911 call of a break-in. Realizing he’s been set up, Garret takes his men into the house and discover that Simon and Sterling knocked out the agents in the back and made their escape.
When Jarvis receives word of what happens, he calls Sophia to make his report that Simon has teamed up with Sterling. She tells Jarvis that their arrangement is over if Martinez recovers, but he wonders if he can trust her. Sophia assures him that if he remains President, the American people will be spared and that he has no choice in any event.
Sterling steals a car and tries to figure out the best way to get the counteragent to Martinez now that Jarvis is on to them. They conclude that their best chance is to contact Christina despite the fact that Jarvis will be watching her.
When Christina returns to her husband’s hospital room, she finds soldiers blocking her way. They inform her that the attorney general has increased the security alert and she isn’t permitted to see her husband. Christina tries to call the attorney general without success, and then receives a call from Sterling saying that they need to meet.
In the Oval Office, Jarvis receives a report from a NSA signal analyst that Sterling made a 24-second encrypted call to Christina. Jarvis orders him to decipher it, but the analyst warns that it will take several hours. Upon hearing that, Jarvis goes to see Christina at the hospital.
Vicky and Sean enter the mall and Sean heads for the roof while Vicky tries to get everyone out.
Roman establishes the video feed to Sophia at the new safehouse. On the roof, Alexandra puts the lung sample into the aerosolizing unit.
In the mall, Vicky discovers that the fire alarms have been disabled. She tries to convince a security guard that she’s a federal agent, but when he hesitates, she grabs his gun and orders him to take her to the security center. Meanwhile Sophia spots Sean on the video feeds and tells Roman to intercept him. Sean gets to the roof and spots Alexandra, but Roman opens fire and drives him to cover. Roman tells Alexandra to keep working while he holds off Sean.
At the hospital, Jarvis meet with Christina and assures her that she was supposed to receive access to her husband. He finally admits that Martinez was poisoned, but blames it on Simon and Sterling. Christina wonders how she can trust him after Coral Gables, but Jarvis insists that he was innocent. The first lady has to admit that she thought Sterling was acting suspicious when he hinted there was more to Martinez’ condition then a stroke, and tells Jarvis that Sterling called her earlier and asked her to meet him and Simon at a warehouse. She gives Jarvis the address and he promises to do everything he can to bring them to justice.
Sophia talks to the captive Leila and tells her that she’s misguided, and that she’s doing what she has to, to save her family. The alien leader then asks Leila what she told Sean, but Leila first denies she said anything and then refuses to say anything further. Sophia leaves, but warns that Leila has doomed Sean just as she doomed Michael by involving him.
In the security room, Vicky and the guard discover that the other guard has been knocked out. The guard agrees to start the evacuation, but warns that it will take 20-25 minutes to get everyone out. He also doesn’t have access to the air circulation controls. The mall pedestrians start heading out of the mall and Vicky helps them along where she can.
Sean manages to sneak around behind Roman and they struggle for the gun. Alexandra hooks up the aerosolizing unit and sets it to go off in three minute and then slips away with the lung samples. Vicky gets to the roof, missing the sleeper agent, and finds Sean just as he turns the gun on Roman and manages to shoot him.
Sterling and Simon enter the warehouse, unaware that the federal agents are watching them. In the Presidential control room, the staff watches the entire thing on spy satellite. Jarvis says that Sterling is now a traitor, meeting with the enemy, and orders an air strike on the warehouse. General Armbruster strenuously objects, and Jarvis tells him to get out if he won’t follow orders. The general leaves and Jarvis tells anyone else who wants to defy him to get out. No one else does so, but Peel points out that Jarvis is conducting an assassination. The President ignores him and orders the Air Force drone to fire a missile at the warehouse. It does, destroying it, and Jarvis tells the commander to confirm the kills.
Alexandra blends in with the crowd evacuating the mall and gets onto a bus. She then opens the case containing the samples.
With time running out, Sean admits to Vicky that he has no idea how to shut down the time. Vicky says they have to leave, but refuses to go when Sean tells her to abandon him. Panicking, Sean finally shoots the timer, destroying it with seconds to spare. Once they confirm the unit is no longer a danger, they search Roman and find his wallet, and then leave.
Alexandra drives the bus to the sleeper safehouse. She apologizes to Sophia for failing to release the sample in the mall, but Sophia assures her that thanks to the video they have on the bus of people dying of the virus, Dr. Lu has what she needs to find a way to spread the disease. Lu calls Sophia in and explains that they need to find a way to mutate the virus so that it is less effective, and proposes that they do so by forcing it to jump into the right species. Once that happens, they can screen for the proper variation. To do so, they need a hybrid, and Lu notes that they have one such hybrid.
At the hospital, Christina goes to the gift shop to get flowers and then enters her husband’s room now that she has clearance from Jarvis. Dr. Reed warns her that they don’t have much time, but Christina insists that she’s not going to give up and tells him to leave.
Garret and his men search the demolished warehouse and find an underground passage leading away. When he gets the information, Jarvis realizes that he’s been played. The signal analyst comes in and informs Jarvis that Sterling called Christina to have her call him later at a phone booth after telling her that Jarvis poisoned her husband. Jarvis realizes that Christina was lying to him earlier and was in on the whole thing.
Christina takes the flowers and removes a syringe with the counteragent, provided by Simon working in the gift shop. She injects Martinez with the antidote and kisses him on the cheek.
Carlos and the others take Leila to a quarantine tent in the safehouse and strap her to a table. As Lu prepares a swab with the Spanish flu virus, Sophia tells Leila that she will now help them spread it across the planet.