Sophia walks through what looks like a post-apocalyptic world. She meets a sick little girl who is close to death. The girl asks for help but then gets increasingly irate and accuses Sophia of killing her and her family. Sophia wakes up in a cold sweat. It was all just a horrible dream. Later, Dr. Lu and Sophia discuss Leila's condition. She is now a carrier of the pathogen. It will take a couple days to kill a human. Within two weeks, it could kill over of the world's population. Within five weeks, over Clearly still shaken by her nightmare, Sophia wonders if her peoples' needs justify this bloodshed.
At the hospital, Christina watches as Martinez's health miraculously improves. It's clear the counter-agent is working! Meanwhile, Carlos tells Sophia that the portal array is almost complete and that their "people" are ready to come to Earth. Carlos has one concern: there's a reconnaissance satellite over Tibet, and he worries that the portal array will be detected. Sophia calls Jarvis and tells him to redirect the satellite. Jarvis reluctantly agrees but tells Sophia that unfortunately Martinez's health is improving. Sophia tells Jarvis to make sure Martinez does not "reenter the equation." Jarvis reminds Sophia that he is only collaborating with her in order to spare the American people from the pathogen.
At a seedy bar, Simon meets with Sterling. They know that Sophia looked for a "super weapon" in Siberia, but it's still not clear to them what this weapon is. Just then, they see a news report about a foiled terrorist plot at a nearby mall. Simon recognizes one of the casualties: it's Roman, a fellow Sleeper. Meanwhile, Sean and Vicky look through Roman's wallet and find his address. They decide to go to Roman's address in the hopes that it will lead them to the courier. Sean and Vicky arrive at a loft and enter. Inside they find Simon and Sterling!
After a tense standoff, Sean and Vicky and Simon and Sterling realize they're all on the same side. They're all just looking for more information regarding Roman and the Sleepers' plot. Sean and Vicky tell Simon and Sterling about the pathogen and the thwarted attack at the mall. Meanwhile, at the underground bunker, Dr. Lu waits as the virus replicates itself in Leila's system. Leila begs Dr. Lu not to kill innocent human life, but Dr. Lu coolly reveals, "We are only taking back what's rightfully ours. We were here first."
Sophia lectures her team about her contamination plan. The viral attack will be three-pronged: Sleepers will contaminate food at a food-processing facility, currency at the Bureau of Engraving in Virginia and innocent civilians at the International Terminal at Dulles Airport. Within five weeks, the vast majority of humans will be dead. Meanwhile, Jarvis makes arrangements for the satellite to be redirected away from Tibet. The NSA analyst says the process will take a couple hours.
Dr. Reed tells Jarvis that Martinez is making a miraculous, unexplainable recovery. Jarvis walks over to tell Christina the great news, but she slaps him before he can finish his sentence. Christina tells Jarvis she knows he poisoned her husband. Just then, Martinez wakes up! Christina tells Martinez that Simon Lee delivered the counter-agent that saved his life. It's clear that Jarvis and Sophia are working together and must be stopped. Martinez says he must talk to Sterling at once.
At Roman's loft, Sean, Vicky, Simon and Sterling look for any evidence that could lead them to Sophia. During the search, Sterling says he recognizes Vicky from her time in the CIA before she went Black Ops. Vicky pretends Sterling's thinking of someone else. Later, Simon tells Sean that Michael's dead, and it's highly likely Leila will be next. Simon finds receipts - all from Maryland - in Roman's trash. While the team wonders what Roman was secretly working on, Martinez calls Sterling. Sterling tells Martinez about the super virus and Jarvis's collaboration with Sophia. Hearing how quickly things have worsened, Martinez tells Dr. Reed he must return to the White House at once. Across town, Sophia's men have arrived at the three contamination sites and are ready to unleash the virus.
Sean hacks into the NSA site in order to see what Roman was doing when he made his purchases. The surveillance footage shows Roman entering an abandoned factory. Meanwhile, at the bunker, Dr. Lu tells Sophia that at 5:30, all three distribution channels will be spreading the pathogen. Dr. Lu tells Sophia that Leila's body is suffering due to the virus, so Sophia tells Dr. Lu to put Leila out of her misery.
Sophia tells Carlos to go ahead and distribute the virus to the contamination centers. In a stolen SUV, Sean, Simon, Vicky and Sterling make their way to the bunker. Simon notices a scroll in Sean's bag. Sean tells Simon it was a gift from Dempsey. It's clear that the scroll has a critical message only Simon can decipher. Simon, Sean, Sterling and Vicky break into the bunker just as Leila manages to overtake Dr. Lu. Sean rushes in and finds Leila. He desperately wants to hold her, but she explains that she's infected. It's too dangerous for Sean to even touch her.
At the White House, Martinez tells Jarvis to leave the premises at once. Jarvis explains that he's working on a peace agreement with Sophia and that everything he's done has been to guarantee the safety of the American people. Jarvis says he won't resign; after all, Martinez has had multiple strokes and isn't fit to be President anymore. Meanwhile, at the bunker, Leila tells Sean that it's possible there's no cure for her illness. She makes Sean promise he'll stop Sophia.
Simon and Sterling interrogate Dr. Lu. When she refuses to tell them her password, Simon threatens to torture her to death. Dr. Lu finally reveals her password, and Sterling begins searching her laptop's hard drive for clues. Meanwhile, at the three contamination sites, Sleepers deliver canisters containing the deadly pathogen. Across town, Sophia calls Gerard and tells him that the satellite has been diverted and it's time to activate the portal array.