Sophia is walking through a city street filled with the bodies of people dead from the Spanish Flu. She spots a young girl locked in a car with her dead brother, and the girl asks Sophia if she’s a doctor. The girl begs Sophia for help and then pounds on the window, blaming Sophia for everyone’s death.
Sophia wakes up from her nightmare at the sleeper safehouse and goes to see Dr. Lu. The scientist explains that they have successfully used Leila’s hybrid metabolism to cause the Spanish Flu to mutate into a form that won’t cause immediate death, but will still kill 98% of the world’s population. Sophia worries that it will kill the entire human race, and Lu admits that there is no way to limit the disease’s lethality. She assures Sophia that if their situation was reversed, the humans wouldn’t hesitate to wipe them out.
At the hospital, Christina waits at Martinez’s bed as his life signs improve. Dr. Reed admits that the President is recovering, but warns that nothing is certain yet.
Carlos informs Sophia that Gerard believes that the NSA spy satellite above Tibet could detect the portal array. She calls to tell Jarvis to reroute the satellite, and he informs her that Martinez is recovering from the assassination attempt. Jarvis asks Sophia to repeat her promise that she’ll spare the American people and she does so. Once she hangs up, Carlos asks her what Jarvis will do when he realizes they’re releasing the Spanish Flu to kill everyone, and Sophia says that by the time Jarvis knows she’s broken her word, it’ll be too late for him to do anything.
Sterling meets Simon in a bar and they try to work out Sophia’s plan. Sterling has learned that Sophia had a team in Russia and that they brought back something on a plane. A news broadcast mentions the attack at the mall and Simon spots Roman’s corpse. He recognizes it as a sleeper alien who worked for Sophia and they leave to investigate.
Sean and Vicky are driving away from the mall and go through Roman’s wallet. They find his address and drive there, and Sean blames himself for letting Alexandra go. Vicky assures him that they had no choice and he made the right decision. They arrive at a warehouse and enter the upstairs apartment. Sterling and Simon are already there and Simon captures Vicky. Sean manages to capture Sterling at gunpoint and they have a brief standoff until Sean realizes that Simon is one of the aliens. Vicky recognizes Sterling, who vouches for Simon, and they agree to compare notes and search the apartment together.
At the safehouse, Lu checks on Leila and confirms that she is dying. As she administers treatment to keep Leila alive for the time being, Leila begs the scientist not to wipe out humanity. Lu tells her that they are taking back what is theirs, and that they were there first.
Sophia meets with her people for the last time and tells them that that they’ll be spreading the Spanish Flu through a food processing plant, the main Bureau of Engraving facility, and Dulles International Airport. Once it is spread nationwide by the first two sources and then across the globe by travelers at the airport, humanity will be wiped out within five days. Sophia asks each of them to honor and mourn the massive loss of life, but to remember that they are doing it for the survival of their people.
At the hospital, Jarvis calls the NSA and orders them to reroute the satellite. The analyst warns him that it will take two hours. Jarvis then talks to Reed, who refuses to breach doctor-patient confidentiality. The President insists that it’s a matter of national security and he has to know if Martinez is fit to take back the duties of the Presidency. Next, Jarvis talks to Christina, who slaps him and loudly yells that he tried to murder her husband, and she plans to bury him. The nurse calls Christina away to see her husband, who is waking up, and he calls for Christina.
Reed conducts tests and admits that Martinez is improving. Martinez asks to talk to Christina privately and she explains what happened. The last thing he remembers is warning Sterling that Jarvis poisoned him, and Christina says that Jarvis is now working with Sophia, and Simon is the one who saved Martinez by bringing the counteragent. Martinez struggles to get out of bed and asks his wife to get Sterling for him.
As the quartet search Roman’s apartment, Sterling mentions Vicky’s past as a CIA agent and how her superiors used her as a scapegoat. When Sterling notes that she supposedly went into black ops, Vicky insists that she’s not that person anymore. Meanwhile, Simon tells Sean that Leila was alive the last time he saw her, but she stayed behind with the dying Michael. They don’t find any of Roman’s papers and figure that he trashed them. However, a garbage truck pulls up outside and quickly run down and tell the garbage man to stop. Going through the papers, they find receipts for stores and gas stations in the town of Aberdeen, Maryland.
As they try to pinpoint the sleeper’s safehouse, Martinez calls Sterling and thanks him for his help and Simon’s. Sterling tells Martinez about Sophia’s plan and Martinez figures that Sophia is playing Jarvis for a fool. Martinez says that he’s going to deal with Jarvis, hangs up, and tells Reed that he’s leaving.
The sleepers prepare the three sites for delivery of the disease. When a supervisor at the engraving plant realizes something is wrong, the sleeper infiltrator, Kroll, shoots him and continues with the plan.
Sean hacks the NSA satellite archive using Peel’s access code, provide by Sterling. They check the satellite footage and discover that Roman visited a particular building, along with many other sleepers.
Lu tells Sophia that Leila could last hours or days, and Sophia tells her to put Leila out of her suffering. She then tells Carlos to give the word to the three teams.
As they drive to the sleeper safehouse, Simon notices the scroll that Dempsey gave to Sean. Simon explains that if Dempsey could read the scroll, he knew more than he was telling about why the sleepers were there and what happened to them. Before he can explain further, they arrive at the safehouse. Vicky approaches the guards and distracts them long enough for Sterling to shoot them dead. Inside, they capture a sleeper worker and force him to reveal who is still in the safehouse. He confirms that they have one prisoner, a girl.
Lu prepares to give Leila a sedative to render her unconscious, so she can kill Leila painlessly with a second injection. Leila manages to break free and they struggle, and Leila injects Lu with the sedative. The others arrive and Leila tells them that Sophia plans to have her teams release the virus at 5:30. When Sean starts to open the quarantine unit, Leila stops him and warns that she’s infected, and if Sean touches her than he’ll be infected as well.
Peel takes Martinez to the Oval Office, and Martinez tells Jarvis that he knows all about his alliance with Sophia. Jarvis insists that he’s working to save the American people, and that the cabinet will have to determine if Martinez is fit to return to duty. He tells Martinez that he’ll make sure that he’s tested to confirm if he’s mentally sound, and points out that his former President is in poor physical condition. Gasping for breath, Martinez has no choice but to back down.
Sean tries to access Lu’s encrypted laptop without success, and then goes to talk to Leila. He insists that there must be a cure and makes plans for what they’ll do when it’s all over. Leila says that they need to focus on finding and stopping Sophia.
Simon wakes up Lu and tries to get through to her, but she refuses to help. He then grabs a drill and threatens to drill and keep drilling until she talks. Lu finally gives up the password and Sterling enters it. They find dozens of distribution plans and have no choice but to go through them one at a time.
The three sleeper teams receive the canisters with the disease and prepare to distribute it.
Sophia calls Gerard and tells him that Jarvis has rerouted the NSA surveillance satellite. He and his team power up the array, opening a portal high above Earth.