On the train, Sophia notices a bag and picks it up. In it is an earbud, and Thomas contacts her. Sophia is angry that he threatened to kill people, and warns that Martinez will be using her to get to Thomas. Thomas has her change clothing with what's in the bag.
Justin Murphy and his team follow the radioactive isotope inside of Sophia as Simon watches. Blake assures Martinez that the tracer will stay active for the next seven hours, and warns that Sophia isn't trustworthy. Martinez insists that she's to be kept alive and goes. Simon asks Blake to let him join his team in the field. En route, Simon calls Thomas and tells him about the isotope, and assures him that he has a way to deal with it.
At Venice Beach, CA, Simon and his girlfriend Violet go to the beach. She notes that he acts like he's never seen an ocean before, and Simon admits that he hasn't. When she wonders about his past, Simon insists that he's free of it now that he's with her. They embrace and assure each other that they love each other, and then Simon looks up to see Thomas standing on the beach.
Simon tells Thomas to have Sophia get off at the next station. Thomas briefs Sophia and she gets off at Chinatown. Simon has his team hold their approach while Sophia enters a coffee shop. She gets a cup of coffee and Simon approaches her. He then secretly pours a liquid into the coffee pots. Blake and his team realize that there are now multiple targets, as everyone in the shop drank the coffee with the isotope that Simon added. In the confusion, Sophia slips away.
Sean, Leigh, and Collier take refuge at a cheap motel. Leigh asks Sean what happened to her family. In the neighboring room, Collier interrogates Carter, who warns that she can't identify him from his fingerprints. He asks for a doctor and tells her she's in trouble, but Collier isn't impressed.
Sean tries to explain what happened, and how Michael told her to run and find her. Leigh wonders what happened to her mother, and Sean explains what Michael told him about her mother's death. She breaks into tears, and Sean admits that the same people that took Leigh took Samantha. Leigh goes to confront Carter and demands to know where Samantha is. He apparently has no idea what she's talking about, and she grabs his bleeding leg. Sean pulls her off, and Carter tells her to blame her father. He warns her that Michael brought it on himself
Simon and his team search downtown Washington and realize they don't have enough manpower to cover all of the suspects. Meanwhile, Sophia walks past a dog that barks at her, while Thomas coaches her in how to avoid the security cameras.
At headquarters, Blake ties all of the CCTV cameras into facial recognition software. Justin warns Blake that whoever dosed the people at the coffee shop used the same isotope, and someone took it from the armory 40 minutes ago. Blake realizes that someone in his organization is a traitor, and Justin tells him that they can use a Geiger counter to detect trace radiation on the hands of the thief. Justin then calls Simon and tells him to pull his men back to base.
Simon walks Violet back to her home and promises to meet her that night. As she goes in, she asks him to bring her sunflowers. Once she's inside, Simon meets with Thomas, who says it's time to go. Thomas says that none of them can stay in one place too long, given their reduced aging. Simon admits that he fell in love, and Thomas warns that if Simon won't go, then he'll dispose of Violet. Simon asks for one last chance to say goodbye, but Thomas tells him it's over.
Justin arrives and meets with Simon in an alleyway, and informs him that they have a traitor. He explains that someone took the isotope from the armory, and Simon asks to do it himself to reassure his men. Justin agrees, but notes that someone needs to check him. Simon knocks Justin out and hides him in the trunk of his car.
As they go back to their room, Sean suggests to Leigh that Carter was messing with him. She wants to go back to her house and search for clues, but Sean advises her to wait until Collier can get her into a safe house. He still needs to clear his name of Greg's murder and find the people responsible, and Leigh insists on going with him.
As Carter asks for an ambulance, Collier hears a noise outside and looks out the window, to see Leigh and Sean driving away. They go to the Buchanan home and Leigh pauses when she sees her mother's blood on the carpet. Leigh starts desperately searching, insisting there must be something there. She finds a case filled with Samantha's baby clothes, and gets an idea. Searching the attic, Leigh finds a folder containing blueprints of the Inostranka center and reports of strange lights in the Alaskan sky. A woman comes up behind them, aims a gun at them, and says they shouldn't be there.
Simon calls Thomas and tells him that his cover is blown. Thomas tells him that it's time to move on, and Simon lashes out in frustration.
Ten Years Earlier
In Washington, Simon and his fellow agent, Mike Garret, are discussing Simon's request to transfer to Alaska now that they've completed training. As they walk past a hotel, an elderly Violet sees him and recognizes him, and wonders why he hasn't aged. Her nurse explains that Violet has Alzheimer's, but Violet insists she knows Simon. He tells her that she has him confused with someone else and walks away.
Blake and his team get a fix on Sophia as Martinez returns. They watch on the monitors as she enters a building, and inform Simon. Simon calls Thomas, who tells him to get there as soon as possible as part of his contingency plan. When Sophia arrives, she says they have a lot to talk about but tells him that she's happy to see him.
The woman demands to know how much they know. When they admit they just found the file, she says it's not too late. Leigh refuses to hand over the file, but Sean offers it to the women. When she comes to get it, he manages to disarm her and Leigh takes the gun and directs the woman upstairs. She introduces herself as Madeline Jackson, a former journalist who lost her job when she discovered that people don't want the truth. She starts to rant about conspiracy theories, and how Michael contacted her two years ago when he saw the lights in the Alaskan sky. The authorities closed down her web site, and Madeline warns that there are higher powers at work than the government. She then tells them about the prison and the detainees, and claims that they're aliens.
Blake confirms that a man entered the same building two hours ago, and Martinez figures that it's Thomas. Blake assures the President that his men will soon have the building surrounded.
Simon breaks into the building and hears over the radio that Blake's men are closing in. He finds them as they prepare to leave via the sewers. Thomas tells him not to worry about it, and the building starts to shake. Above, Garret leads a FBI team in and they notice the shaking.
Sophia wonders what Thomas has done, and he tells them that it's time to go. When Sophia objects, he warns that there's nothing they can do. Thomas leaves and Sophia insists that Simon has to go with them. He says that he can't.
Ten years earlier
Simon comes to see Violet, bringing her a sunflower. She wonders if he's an angel, and Simon says he's far from that. He asks for her forgiveness, and Violet explains that she waited for him. She wonders if he loved her, and he assures her that he never stopped.
Sophia begs Simon to come with her, and then falls into the sewers due to a tremor. Simon contacts his men and tells them to evacuate, and then climbs up. He tries to make his way out and spots an injured agent. As he goes to the man's aid, a vast glowing vortex opens in the floor. Garret arrives and together they haul the man out. Simon is hit by debris and tells Garret to keep on going. He tries to follow but is buried in the debris.
Martinez and the others watch on the monitor as the building collapses, leaving flickers of energy and a huge crater.
Garret searches the debris and looks back at where Simon fell… directly within the new crater.