Sophia is walking through a street filled with infected corpses. She comes to a car and a young girl is locked inside. The girl, dying of the virus, wonders if Sophia is a doctor and begs Sophia for help. She then blames Sophia and pounds on the window...
... and Sophia wakes up at the new safehouse. She goes to see Dr. Lu, who explains that Leila's hybrid system mutated the virus and slowed down its fatality rate. They now have a virus that will kill 98% of the world's population. Sophia doesn't want to kill all of the humans, but Lu warns that the pathogen is uncontrollable and it's all or nothing. The doctor warns that the humans would choose the virus if the situation were reversed.
At the hospital, Christina notices that her husband's life signs are improving. Dr. Reed confirms that Martinez is improving, but warns Christina that it may be anomalous.
Carlos reports to Sophia that Gerard is concerned that their portal array in Tibet could be detected by NSA satellites. She calls Jarvis and orders him to reroute the satellite, and Jarvis warns that Martinez is recovering. He asks Sophia to reiterate her promise that she'll spare the American people, and Sophia assures him that they will survive. As she hangs up, Carlos wonders what will happen when Jarvis realizes the virus has been released, and she says that by then, it will be too late.
Sterling and Simon meet in a bar and try to figure out what Sophia is up to. They know about her operation to Siberia and the fact that it was brought back on the plane. As they talk, they hear a news broadcast about the attack at the mall and Simon spots Roman's corpse, and realizes that he was there on Sophia's behalf.
As they drive away, Vicky and Sean go over Roman's wallet and find an address. Sean is concerned that they let Alexandra go, but Vicky insists that they made the right decision at the time. They arrive at the address, a clothing plant, and ask the workers if they've seen anyone. Drawing their guns, they go to the upstairs apartment and split up. Simon and Sterling are there, and Simon captures Vicky. Sean gets the drop on Sterling and the two sides are at a standoff. Sean recognizes Simon as one of Sophia's people, and Sterling vouches for him. Vicky recognizes Sterling and they compare notes. Simon lowers his gun and they start searching the place together.
At the safehouse, Lu checks on Leila's status. Her body signs are dropping and Lu orders treatment to keep her alive for the moment. Leila begs Lu not to kill billions, but Lu says that they're only taking back what is theirs and that they were there first.
Sophia tells her people that they'll spread the virus through three parallel distribution channels: a food-processing plant, the Bureau of Engraving facility, and Dulles Airport. Within five days, the majority of the human population will be dead. Sophia tells them that it will be the last time that they meet as a group, and asks each of them to honor and mourn the loss of life, but remember that they are doing it for their survival.
At the hospital, Jarvis calls in to reroute the satellite. The tech warns that the repositioning will take two hours. Jarvis then meets with Reed, who says that he's cautiously optimistic even though they're not sure what is happening. When he invokes patient-doctor confidentiality, Jarvis says that it's a matter of national security and he wants the transition to be as smooth as possible. Reed says that stroke recovery can take years, but Martinez's case is atypical. Once Reed leaves, Jarvis talks to Christina, but she slaps him and loudly accuses him of poisoning her husband. She threatens to tell everyone and bury Jarvis, and the nurse informs Christina that Martinez has woken up. She goes to her husband's bedside and he is able to open his eyes. He calls for Christina, as Jarvis nervously looks on.
Later, Reed continues his tests but Martinez asks for time alone with his wife. Reed gives them time alone and they kiss, and then Martinez asks what happened. Christina tells him to wait, but Martinez remembers telling Sterling that Jarvis was involved in the attempt on his life. He insists on his wife telling him what she knows, and Christina tells him that Jarvis is working with Sophia, and Simon provided the counteragent. Martinez tries to get out of bed, insisting that he needs to talk to Sterling. He asks Christina to get Sterling for him.
As they search Roman's apartment, Sterling says that he remembers Vicky as a CIA agent that went rogue. Rumor had it that she was scapegoated and started running black ops, but Vicky denies it, saying she doesn't know anyone like that anymore. Meanwhile, Sean asks Simon if Leila could still be alive. Simon says that Leila was alive the last time he saw her, and she stayed behind to help Michael when he was shot. Sean promises to find Leila no matter what he has to do. They find nothing and figure that Roman trashed any personal notes. They hear the garbage truck pull up outside and run down to stop it before it can take Michael's trash. The four of them go through the papers and find receipts to a location in Maryland.
As they search, Martinez calls Sterling and thanks him and Simon for saving his life. Sterling tells him of Sophia's plan to make room for her people by using a virus to wipe out humanity. They figure Jarvis being played for a fool, and Martinez says that he'll deal with his vice-president. He then tells Reed that he's going to the White House, ignoring the doctor's objections.
Lu supervises the loading of the virus canisters, while Carlos confirms everyone is in position at the infection sites.
At the engraving facility, a supervisor realizes something is wrong, but the sleeper in charge, Knolls, shoots him dead. The three groups call in to report that they're in place.
Sean hacks the NSA satellite archives. Sterling provides Peel's access code and they track activity in Aberdeen, Maryland. The spot Roman and track him to an underground facility, and confirm that sleepers have gone in and out regularly.
Sophia asks Lu about Leila's condition, and Lu says that she could have hours or days. When she realizes that Sophia is suffering, Lu says that Leila's pain will only get worse. Sophia tells her to quickly and painlessly end Leila's life.
Carlos prepares to ship the canisters to the three teams, and Sophia gives the word.
As they drive to the facility, Sterling warns that he's called in reinforcements but it will take time. Simon notices that Sean has the scroll that Dempsey gave him, and Sean admits he doesn't know what it says. He asks Simon what he knows, and Simon says that if Dempsey could read the scroll, he knew more than he was telling about why the sleepers were there and what happened. They arrive at the building and prepare to go in.
Lu prepares to give Leila a final, lethal injection.
Vicky approaches the guard station and claims that she's run out of gas. Sterling shoots them down and the group heads inside.
Lu assures Leila that there will be no pain, and the first injection will put her out so she won't feel the effects of the second one.
The quartet captures a sleeper and confirms that there are five of his people inside and a prisoner, a girl.
Inside the protective tent, Leila manages to free herself from the straps and knocks Lu down. They struggle and Leila injects Lu with the syringe intended for her. Sean and the others arrive and Leila tells them that Sophia is going to release the virus at 5:30. When Sean tries to free her, Leila tells her that she's infected as well and that if Sean touches her, he'll die.
Peel escorts Martinez into the Oval Office, and Martinez orders Jarvis out of the office. He tells Jarvis that he knows all about his alliance with Sophia, and Jarvis insists that he's negotiating a peace treaty to guarantee the safety of the American people. When Jarvis says that he's the President, Martinez warns that he won't be for long. However, Jarvis says that there will have to be a vote to determine if he's capable, and he'll have tests to determine if he's mentally sound.
Sean tries to hack Lu's encrypted laptop without success, while Simon and Vicky prepare to interrogate Lu. As they tie her up, Sean goes to see Leila and insists that there must be a cure. He starts discussing what they should do when it's all over. Despite her doubts, Leila goes along at first, but tells Sean that he has to find Sophia and stop her.
Simon wakes up Lu and tells her that she knows deep down that what she's doing is wrong. He asks for the password for the laptop, but Lu insists that it's pointless and refuses. Simon picks up a drill and explains that he'll keep cutting her until she slowly bleeds to death, but he'll keep her alive to suffer. She finally gives him the password and Sterling confirms that it's the correct code. There are dozens of distribution scenarios and they can't trust anything Lu tells them, so they go to work on their own.
Sophia's teams receive the virus canisters and begin distribution.
Sophia calls Gerard to confirm that the satellite has been redirected, and tells him to power up the array. Gerard and his team start up the portal and a wormhole opens in space above Earth.