At the sleeper safehouse, Sean talks to Leila, who is within the quarantine tent, and informs her that Sterling has called in a medical team to help her. Leila warns that it’s too late but her boyfriend refuses to accept it. She tells him to make sure that Samantha is okay and passes out as the medical team arrives. The head doctor assures Sean that they’ll do everything they can for Leila. Sean then checks with Sterling, Simon, and Vicky, who have found Sophia’s distribution plan for the virus on Dr. Lu’s laptop.
As they drive to Dulles, Sophia and Carlos hear from Aaron and Devon, who are commanding the teams at the food processing plant and the engraving facility. Sophia checks the time and then tells Carlos to pull over, explaining that it’s safer. The ground shakes and a bright light fills the air. Once the tremor stops, Sophia tells Carlos that Gerard had warned her that the tremor would occur when he activated the portal to create a wormhole in space. She appears to hesitate and Carlos reminds her that they’re fighting for the survival of their paper. Sophia nods and says that she can’t afford any self-doubt if they’re to save their people.
As Peel and Martinez watch a broadcast about the tremor, Sterling calls and tells them what he’s learned of Sophia’s plan. He asks Martinez to send in counter-terrorist teams, but Martinez explains that he hasn’t regained the Presidency yet, and can’t until the cabinet votes in his favor. However, Peel can use a written order to bypass Jarvis and send counter-terrorist teams to the food processing plant and the printing facility. However, they can’t shut down the airport. Sterling and his group head for Dulles to prevent her from releasing the virus.
Martinez talks to Jarvis, but the current President refuses to concede and says that Martinez won’t win the cabinet vote. Martinez insists that they have to deal with the airport crisis, but Jarvis figures that he’s trying to make him appear as a fool and undermine him before the cabinet. With time running out, Martinez offers to withdraw as the President and remain silent about Jarvis’ scheme as long as Jarvis stops Sophia. Jarvis refuses and boasts that Martinez can’t expose him without convincing the cabinet that he’s deranged.
Jarvis goes to the Oval Office and calls Sophia, and asks if there’s any substance to Martinez’s claim. Sophia assures Jarvis that she’s working for their common good and that if Jarvis can hold off Martinez for one more day, then he’ll secure his position as President and they’ll both be safe. Sophia then hangs up and tells Carlos that they know about her scheme. They go to a hanger and pick up airport IDs from a fake customs officer and sleeper agent, Eddie Delgado. Sophia says that once they have the canisters, they’ll release the virus immediately and infect the airport.
Volcanoes come alive as more tremors shake the planet. As they watch the news, Peel briefs Martinez’s on Sterling’s plan and warns that the odds aren’t good. Christina worries that Martinez can’t handle the stress of confronting Jarvis, but her husband insists that he has no choice.
Government commandos move in on the two distribution facilities and take out the aliens, stopping them from releasing the virus.
Sean and the others arrive at Dulles, and Peel calls to tell them that Martinez hasn’t retaken the Presidency yet and they’re on their own. Sean has the information from Lu’s laptop and knows where Delgado is bringing in the canisters. Sterling and Simon go to intercept Delgado while Sean and Vicky enter the terminal and try to find Sophia.
Delgado hides the canisters beneath a contraband cart and takes it in past a security guard who knows him and doesn’t question what he’s doing.
Sophia and Carlos enter the airport and have to pass through a security checkpoint. The alien leader is pulled aside for a TSA check, but they don’t find anything. Once she’s released, Sophia takes a call from Devon, who reports that they’ve failed to release the virus at the other two sites. As she listens, Devon is gunned down by soldiers.
While the cabinet prepares for the vote, Peel informs Martinez of the soldiers’ success at the two sites. Martinez enters the cabinet chamber and receives a round of applause, but then falters and finally collapses.
Sterling and Simon find the security guard and ask him if they’ve seen Delgado. When he refuses to help them unless they provide ID proving they are who they say, Sterling draws a gun on him and forces the guard to open the door.
Sophia and Carlos use the security card from Delgado to get back into the cargo area to meet with him. Meanwhile, Simon and Sterling spot Delgado and a shootout begins. The two men split up, but Delgado first shoots Simon in the leg and then the chest. He gets away while Sterling checks on Simon and confirms that his Kevlar vest protected him from the second shot. The director then calls Vicky and Sean and tells them to intercept Delgado. They knock out a guard and gain access to the secure area.
Delgado meets with Sophia and Carlos and gives them two of the three canisters. Sean and Vicky arrive and shoot, killing Delgado. Carlos tells Sophia to deliver her canister while he holds off the others. Sean goes after Sophia while Vicky uses a wheeled cart to get to Carlos. She wounds him in the leg and he tries to activate his canister, but Sterling arrives in time to shoot and kill him before he can succeed.
Jarvis informs the Speaker of the House that they have to deal with the immediate crisis, and she starts to withdraw Martinez’s petition for reinstatement. However, Christina and Peel bring in Martinez, who tells them to begin. Jarvis begins by claiming that he’ll relinquish the Presidency once Martinez is capable of the position. However, he hands out dossiers on Martinez’s medical status and the fact that he’s left the hospital despite his doctors’ objections. Jarvis insists that they have to do the right thing. Martinez then speaks, telling the cabinet that Jarvis has brought them to the edge of extinction because of his thirst for power, and that he’s working with Sophia. He accuses Jarvis of poisoning him, a charge that Jarvis denies. Jarvis insists that Martinez is lying, but Martinez plays a recording he secretly made of their earlier conversation in the hallway. Jarvis claims that the tape is a fake, but Martinez takes command tells Pell to reinstate Armbruster and Sterling.
Sean spots Sophia and chases her through the terminal, but she locks herself in a room and prepares to activate her canister. Meanwhile, Vicky tries to find Sean and realizes that Martinez has given the order to cancel all flights and seal the airport. She goes to tell Sean, warning that they can’t evacuate while the building is sealed. As Sophia prepares to activate the virus, Sean tries to get through to her, insisting that she isn’t a murderer and that she once stood for a peaceful resolution to the situation between the two races. Sophia reminds him that her son died along with the others on the two busses, and insists that Sean doesn’t know her. Sean reminds her that everyone has suffered pain and loss, and that there has been enough suffering. Sophia finally hesitates, and then shuts down the canister and unlocks the door.
Leila’s doctor tells her that Sean and the others stopped the release of the virus. However, she then informs Leila that they discovered something unusual in her test results.
The hazmat teams confirm that Sean is clean, and Simon warns Sean that they haven’t stopped the plan to bring the remaining two and a half billion aliens to Earth. He then tells Sean that their people were on Earth first and that they left to avoid transformation by something known as The Event, which would have caused them to evolve to a higher stage of life... and wipe out all humanity in the process. Sean asks him for more information, but Sterling calls Simon away to the White House. As they go, Simon tells Simon that all the answers that he needs are in the scroll that Dempsey gave him in France.
Sterling and Simon quickly take a jet to the White House and the Oval Office. Martinez thanks Simon for saving him and says that they’ll discuss the rest of his activities later. They try to figure out how to stop the portal, and Simon admits that he only knows that it’s somewhere in Asia. Peel recalls that Jarvis had a NSA satellite rerouted and they have the NSA move it back over Tibet. Once it’s in position, they spot the portal and Simon confirms that it’s been activated. Martinez contacts the Chinese, who refuses to bomb the site without solid evidence that it poses a threat. Simon admits that he doesn’t know how to stop it, and Peel confirms that the army is bringing Sophia to the White House.
Sean goes to the hospital to see Leila and Vicky brings him some coffee. As he starts to thank her, the doctor arrives to tell Sean that he’s been cleared to see Leila. He starts to go, and Vicky thanks him for giving her the chance to change who she was and protect her family. They hug, and Sean awkwardly says his goodbyes to her. He enters Leila’s room and assures her that the doctors will cure her. She then tells him the results of the tests: she’s pregnant. Sean promises her that she and the child will both be okay.
When Sophia is brought to the Oval Office, she tells Martinez that there’s no way to shut down the portal, and explains that she planned to wipe out humanity with the virus, because the alternative when her people arrive is far, far worse. As tremors shake the planet, Sophia tells Martinez that it’s too late and that she’s sorry. Everyone runs outside and looks up as the portal opens and Sophia’s people arrive: all 2.5 billion of them, along with their home planet. As Christina embraces her son, David, he asks what the new object in the spy is and she tells him, “Home.”