Sophia boards the train and rides it, and notices a bag on the seat nearby. She goes to it and finds an earbud inside. Thomas contacts her and she snaps at him, wondering what he was up to. She warns him that Martinez is tracking her, and Thomas tells her to put on the clothes in the sack, and then wait for further instructions.
Blake's team continues to track Sophia, using the radioactive isotope that they secretly gave her in her food. They have seven hours until the isotope goes inert. Martinez insists that they don't harm Sophia despite Blake's warning that she's not trustworthy. Martinez leaves and Simon asks for permission to oversee is agents in the field. Once he's outside, he calls Thomas and tells him about the isotope. Simon explains that he has a way to deal with it.
At Venice Beach, CA, Simon visits the beach with his girlfriend, Violet, who knows him as Mason. He says that there wasn't any water where he came from, and explains that he doesn't care about his past when he's with her because he's free of it. As they embrace, Simon sees Thomas down the beach, waiting for him.
Simon tells Thomas to direct Sophia to a particular address. She gets off at the next station and makes her way to a coffee shop. Simon keeps his team back, goes inside, and pours some of the isotope in each coffee pot. Once people start drinking it and then leave, Blake's people get dozens of radiation signals going in all directions.
Collier, Sean, and Leigh take their prisoner to a cheap hotel. While Collier interrogates Carter in one room, Leigh and Sean have a reunion in the other. She asks him what happened to her family. Meanwhile, Carter refuses to say anything, and warns that Collier will be unable to ID him from his fingerprints. He asks for a doctor but Collier refuses and warns that if he dies, she'll have problems.
Sean tries to explain how the plane was teleported to Arizona, but Leigh notes that it doesn't make any sense. She wonders if her mother is looking for Michael, and Sean finally tells her that her mother is dead and Samantha is still missing. Leigh goes to see Carter and demands answers, but he apparently has no idea who Samantha is or where she is. She tortures him by jabbing his wound, and Sean pulls her off. Carter tells her that her father is the one who got his family involved and brought things down on himself.
Simon goes back to the coffee shop, pretending to get there for the first time, and meets with fellow agent Mike Garret. Garret figures that one of Thomas' people got there before, and they lock down the coffee shop claiming a homeland security threat. Meanwhile, Sophia makes her way through the streets and avoids the CCTV cameras and barking dogs.
Back at headquarters, Justin informs Blake that the person who doses the people at the coffee shop used the same isotope they did. He checked on the stockpile, and someone took the isotope from the armory 40 minutes. The records show that someone on the field team had access, and Justin can use a radiation detector to detect residual radiation on the guilty party's hands. As he goes, Justin calls Simon and tells him to pull in his men because he has a problem.
Simon drops Violet off at her house, and she asks him to bring her sunflowers later. He then goes to meet with Thomas, who says it's time to move on before someone notices that Simon isn't aging. Simon admits that he fell in love, but Thomas tells him that either Simon goes or he'll dispose of Violet. When Simon asks for a last chance to say goodbye, Thomas tells him that it's over.
Justin arrives and parks in an alleyway, and Simon informs him the team is out front. When Simon hears Justin's explanation of what happened and how he can detect the traitor, he offers to do the tests himself. However, Justin notes that he'll still have to check Simon. Simon knocks him out and dumps him in the trunk of his own car, and then drives away.
Sean warns Leigh that Carter is trying to mess with her, but she insists on going to her parents' house and finding something that connects Michael to the conspiracy. However, Sean wants her to stay until Collier can get her until a safe house, and he needs to find the people behind it to clear his name. However, Leigh insists on going with him. A few minutes later, they drive away before Collier can stop them.
Sean and Leigh go to the Buchanan home and begin searching. Leigh finds a box with Samantha's baby clothing, and then suggests they search in the attic. She finds a folder containing blueprints of the Inostranka facility, and newspaper clippings about mysterious lights in the Alaskan night sky. Before they can figure out what it means, a woman comes up behind them with a gun and says they shouldn't have come there.
Simon calls Thomas and tells him that he was forced to subdue Justin, and there was no point in killing him. Thomas tells him that it's time to move on, and Simon hits the car roof in frustration.
Ten Years Earlier
As Garrett and Simon walk down the street after graduation from the FBI academy, they pass a building and an elderly woman calls out to Simon, using his assumed name of Mason from 1954. It's Violet, now in her 70s and suffering from Alzheimer's. He insists that she is mistaken and leaves.
Blake's team uses the CCTVs to spot Sophia entering a building ten minutes ago. Martinez arrives and Blake gives him an update. When Simon gets the report, he calls Thomas and tells him to get out, but Thomas says he has a contingency plan and Simon needs to meet them.
Sophia finds Thomas and warns that they have a lot to talk about, but first embraces him and admits it's good to see him.
The woman demands to know how much they've seen of Michael's file. Sean starts to hand it over, but Leigh insists that they'll keep it. As the woman approaches, Sean refuses to endanger Leigh and offers the woman the file, and then manages to disarm her. They demand answers and the woman explains that she's Madeline Jackson, a former journalist. She rants about how she discovered a vast conspiracy. Madeline explains that two years ago, a storm forced Michael to fly over Inostranka. He spotted the facility, and then read an article on Madeline's web site about the lights. Madeline warns them that the government is nothing compared to the forces that want it kept a secret. When the conspiracy realized that Michael knew too much, they took him. Sean asks her to explain what Michael knew, and she tells them how in 1944, an aircraft crashed and the government imprisoned the passengers... who were aliens.
Blake checks the archived tapes from the CCTVs and determines that a man who Martinez assumes is Thomas entered the building. Meanwhile, Simon breaks into the building via a side door as he hears a radio broadcast that Garret and his FBI agents are on the way. Simon continues to search for the others. He finds them in the basement, preparing to leave through the sewer. Thomas tells him not to worry, and then the building starts to shake. Sophia wonders what Thomas has done, and he insists that it's too late to call it off. He climbs down into the sewers and Sophia tells Simon that he has no choice but to come with them or die.
Ten years Earlier
Simon comes to see Violet, who still recognizes him. He brings her a sunflower and admits that he loved her, and if it had been up to him, he would have been willing to grow old with her and have children. Violet says that it was up to her.
Simon ignores Sophia's last plea and alerts his men to evacuate, while she drops into the sewers. He climbs up the ladder and heads for the exit, dodging debris. Simon spots a trapped FBI agent and goes to help him. There's an unearthly roar and a huge gaping vortex opens up in the floor behind him. Garret comes to help and they head for the exit. Simon is knocked down by debris and tells Garret to go ahead with the injured man. Just as Garret gets clear, the building collapses.
In the command center, Martinez and Blake watch as the building crumples in a matter of seconds.
Garret goes back to where Simon was... and where there is now only a vast crater and piles of debris.