An injured Sterling meets with Martinez and his staff at the White House. Martinez harshly scolds Armbruster for losing track of Thomas and the detainees. Martinez - clearly still shaken by his nightmare - goes so far as to call Armbruster incompetent. Simon phones Sophia with news that Thomas murdered the detainees who wouldn't swear allegiance to him. In other words, Thomas mercilessly killed 44 of Sophia's followers. Angered, Sophia says that Michael has located Thomas' right hand man, Hanson, in San Francisco. It's payback time. Meanwhile Michael leaves Leila and Samantha in the care of Diane and Carlos Geller, a couple living in an eerie, quiet home. Later, Carlos gives Michael a shotgun. Then Michael and Sophia drive off to find Hanson.
Hanson enters a seedy store carrying a bag of money. He hands the cash to a worker - clearly he's laundering money - before noticing Sophia heading towards the store. Hanson rushes out the back door when suddenly Michael and Sophia ambush him! When Hanson won't reveal Thomas' whereabouts, Michael puts him in a nerve hold. In excruciating pain, Hanson reveals that Thomas is trying to steal uranium from a California nuclear plant in order to power the portal array. But how will Thomas get past security?
Sophia phones Martinez and tells him that Thomas is planning to portal uranium rods out of the San Onofre nuclear plant, near San Diego. The uranium will create a portal that will bring more of her people to Earth. The last time Thomas attempted this, it resulted in Chernobyl, the largest environmental disaster of all time. When Martinez asks why he should trust Sophia, the keeper of so many secrets, she responds cryptically, saying "Everything I've kept from you was to protect you." Meanwhile, Samantha notices Leila hide a picture of her and Sean. When Samantha asks if Leila misses Sean, she admits that she does.
At a bar, Sean notices an abusive boyfriend shoving his girlfriend. When the guy pushes Sean, Sean beats him to a bloody pulp. Later, Sean breaks into his sister Michelle's house. Michelle is shocked to see her brother and asks what's going on. After Sean tells her of the evil people targeting him, Michelle asks why he's running away. The question resonates with Sean. At the White House, Sterling tells Martinez that Thomas' "portaling" technology could cause death, birth defects, and cancer to spread in neighboring populations. Having seen that some of the sleepers, such as Maya, are well-intentioned, Thomas urges Sterling to believe Sophia's warning and move the rods before Thomas can get to them.
At the San Onofre power plant, Simon tells Ellington, the manager, to power down. After that, they will have to remove the fuel rods from the core and transfer them to another location. As the process begins, Simon calls Sophia to tell her that they're about transfer the uranium into the casks. They're also locking down the facility so when the portal opens, no radioactive material will be released into the atmosphere. Hanson overhears Sophia's conversation with Simon. Hanson pulls a device out of his face and uses it to phone Thomas. Hanson tells Thomas that Sophia bought his false story: as a result, the uranium will be transferred out of San Onofre at which point Thomas can steal it! It was a trick!
Leila overhears Carlos and Diane Geller having a fierce argument over whether they should support Sophia or Thomas. Carlos fears what Thomas is planning to do to Earth's "native population." Leila barges in, asking to know what evil plot her father is trying to stop. Carlos refuses to divulge the details, claiming Leila is half-human, and therefore not totally one of them. Outside a supermarket, a man follows Vicky to her car. She ambushes him and demands to know who sent him. He says he was just returning a receipt that fell from her wallet and then runs off. Moments later Vicky arrives home with her groceries. Suddenly Sean appears brandishing a gun. He's not there to kill her; he wants to team up with her to stop the men who hired her.
With Hanson handcuffed to a pipe, Michael decides it's safe to step out for a quick bite to eat. As soon as he leaves, Hanson frees himself! He sneaks up on Sophia and attacks her. Michael appears just before it's too late and shoots Hanson! Sophia notices Hanson's communication device on the floor and realizes he must've contacted Thomas.On a highway, Simon drives in a convoy surrounding a truck carrying the uranium. Suddenly, a huge explosion goes off! Gun-toting masked men appear on the hillside, firing on the cars! Thomas and his men take control of the truck but can't find where Simon went.
At the Oval Office, Sterling tells Martinez that the convoy transferring the uranium rods was attacked in transit. Their men are dead and Thomas no doubt has the rods. Sterling guesses that Thomas was never planning on "portaling" anything, he was just waiting for the uranium to leave the plant! Sophia calls Martinez and tells him that she too was tricked by Thomas and Hanson. Martinez says she should turn herself in to prove her pure intentions. She refuses, saying she needs more time to stop Thomas and hangs up. Sterling, however, was able to trace the call to San Francisco. Martinez orders his men to get Sophia - and to kill her in the process if they have to.