Sophia finds a communication device and a change of clothes on the subway. Through a small ear bud, Sophia harshly condemns Thomas' actions, saying it was wrong to endanger almost 200 peoples' lives. Meanwhile, intelligence analysts - including Simon and Sterling - track Sophia's progress by monitoring a radioactive isotope that was hidden in her food and is circulating in her bloodstream. Martinez reminds Sterling that Sophia is to remain unharmed; at this point her sole purpose is to lead them to Thomas. Sterling reluctantly agrees not to harm Sophia. Simon asks to supervise the operation from the field, stating that he'd like to work closely with agents on the ground. Once on the road, Simon calls Thomas and warns him that Sophia's being tracked.
We flash back to Venice Beach where Simon and his beautiful girlfriend Violet enjoy their picturesque surroundings. When Violet inquires about Simon's past, he changes the subject, saying that when he's with her, the past disappears. Overcome with emotion, Violet says, "I love you Mason." Nearby, Thomas watches Simon with a disturbing look in his eyes. We're back to the present. Simon advises Sophia to make an abrupt exit from the subway and enter a coffee shop. Once there, Simon laces carafes of milk with the isotope. Suddenly the government officials lose track of Sophia as multiple patrons leave with the isotope in their system.
At a motel, Sean tells Leila the sad news about her family: her mother is dead and her father and sister are missing. Overcome with emotion, Leila charges into a neighboring room where Agent Collier has been unsuccessfully interrogating Carter. Leila demands that Carter tell her what happened to Samantha. Carter plays dumb and tells Leila that if she wants someone to blame, she should blame her father. "You didn't know?" Carter adds. "He's no angel. He brought this on himself." Outside the coffee shop, Agent Garret tells Simon that they've lost Sophia amid numerous false targets. They decide to lock down the coffee shop and patrol the nearby areas. Sophia walks down the street aided by Thomas' instructions. A dog loudly barks at Sophia, startling her.
At the White House, Sterling asks agents to check camera footage near the coffee shop. Perhaps facial recognition technology will lead them to Sophia before she gets lost among the decoys. Sterling's aide Murphy reports that Scandium 46 - the rare isotope used on Sophia and the other coffee shop patrons - was taken from the government armory. That means they have a mole! Luckily the isotope would've left trace amounts on the traitor; all Sterling has to do is check all of his men. Murphy calls Simon and tells him to keep all the agents at the coffee shop. There's been a problem and Murphy's going to get to the bottom of it.
We flash back to a seaside bungalow where Violet asks Simon (a.k.a. Mason) to buy dinner and some sunflowers so that they can have a romantic evening indoors. Simon heads off to the market and encounters Thomas. Thomas tells Simon that it's time to go. Thomas reasons that if Simon stays in any one place for too long, people will start to notice that he's not aging. Simon reluctantly agrees, but is clearly heartbroken over the fact that he has to leave Violet - his one true love - without even saying goodbye. Murphy tells Simon that he has to test all his field men for trace levels of Scandium 46. Simon asks to test his men himself, arguing it would look better coming from him. When Murphy asks to test Simon himself, Simon knocks him out and puts his body in his trunk.
At the motel, Leila can't get Carter's words out of her head. What if they chose to terrorize her father for a reason? Leila wants to investigate what happened to her family but Sean argues that Leila should wait for Collier's ex-husband to arrest Carter and to hide Leila in a secure location. Leila disregards Sean's advice, stating that she doesn't want to rest, she wants to investigate. Sean gives in and together they drive to the family's house to search for clues. Now a crime scene, the Buchanan house is empty and eerie. Leila searches the attic and finds newspaper articles about the 1944 Alaskan air crash and Inostranka blueprints. Suddenly a woman enters the home saying, "You shouldn't have come here."
Simon calls Thomas and tells him that his cover's blown. Thomas tells Simon that since he didn't actually kill Murphy, Simon must move on and create a new identity. We flash back to a city street where Simon and his friend Mike have just completed basic training. Mike wants to celebrate before Simon's stationed in Alaska. A woman's voice calls out to Simon. "Mason? It's me." Simon turns around and sees Violet, now an old woman. Simon pretends not to know her. A young lady standing beside Violet apologizes for the elderly woman, claiming she suffers from Alzheimer's disease. Simon walks away, burying deep heartbreak and regret.
Sterling tells Martinez that investigators have just pulled up video camera footage of Sophia entering a building. Overhearing the bad news, Simon phones Thomas and tells him that Sterling's spotted Sophia. Thomas tells Simon to relax and join them at the nondescript building. Thomas claims he has a contingency plan but won't elaborate further. Meanwhile, inside the building, Sophia finally meets up with Thomas. She tells him they've got a lot to talk about but for now she's just happy to see him. She kisses him tenderly and hugs him.
At the Buchanan house, an armed woman demands that Leila and Sean hand over Michael's top secret file. Sean overpowers the woman and takes her gun. The woman identifies herself as former journalist Madeline Jackson. She claims that two years ago, Michael contacted her, stating that he had seen a strange government facility while piloting a diverted flight over Alaska. Madeline's convinced that Michael's been targeted by unseen forces for knowing too much about Inostranka. That is, Michael knows that in 1944 extraterrestrial biological entities (E.B.E.'s) crashed onto Alaskan soil and have been detained in Inostranka ever since. Sean and Leila look dumbfounded. Is this woman completely out of her mind?
At the White House, Sterling shows Martinez a blurry, faraway image of Thomas entering the building two hours before Sophia arrived. Simon sneaks into the building moments later, breaking through a back door so as to avoid security camera detection. Simon finds Sophia and Thomas and warns them that they're surrounded by F.B.I. agents. Thomas tells Simon not to worry. Suddenly the building starts shaking. Thomas convinces Sophia to follow him through a compartment in the floor. Simon, however, insists on staying. Sophia begs him to come with them but Simon resists. We flash back to a hospital room where Simon stands beside an ailing, elderly Violet. He's brought her a solitary sunflower just like she asked many years before. Simon begs Violet to forgive him for abandoning her all those years before.
We're back to the present. Simon evacuates the shaking building in order to save everyone's lives. Simon assists an injured F.B.I. agent as the building crumbles around them. Debris can be seen sinking into a strange white light. Suddenly an explosion launches debris everywhere and Simon is trapped in the rubble. Simon insists that his colleagues continue evacuating and leave him behind. At the White House, Sterling and Martinez watch in real time as the building implodes in a heap of dust and ash! All that's left is a huge crater-like hole. There's no sign of Simon.