Meanwhile, Leila forces Michael to come clean about the true story of his past. He admits to being from a place "very far away" called NGC 253. He and his people left because life was no longer sustainable. Some of his people were imprisoned while others became sleepers. Then Michael makes a shocking pronouncement: he and Leila must leave but Sean can't come with them. It's Sophia's order. At Inostranka, Thomas speaks to the detainees and takes credit for freeing them when all Sophia ever offered was cheap talk. He announces his formal cessation from Sophia and says humans should serve them and not vice versa. While Thomas speaks, Sterling and Bell ambush a sleeper in the command room and take over!
With the phones down, Sterling and Bell are forced to strategize. On a monitor, they see Thomas speaking to the detainees. Sterling suggests they lock down every sector so it is impossible for anyone to leave Inostranka. Bell supports the idea but worries that he and Sterling will surely be killed by Thomas and his men if the prison is locked down. Meanwhile an older detainee tells Maya that he and some others want to stay at Inostranka out of loyalty to Sophia. Maya reluctantly follows Thomas' orders and heads to the exit. She doesn't think it's the right time to go against Thomas. At the exit, Thomas realizes they've all been locked in. He sends his men to get Sterling from the Control Room.
On the monitors, Sterling and Bell see armed sleepers heading for the Control Room. Sterling and Bell flee, coming upon a room full of detainees who've been shot! Their only crime was supporting Sophia. TV host Chris Matthews has Senator Lewis on his show to discuss transparency in government. Namely, she tells the public about the millions of tax dollars being used for a secret government program in Alaska. At the White House, Martinez watches the program in horror. Martinez phones Lewis and tells her that he'll reveal who the Inostranka prisoners are as long as she stops talking to the media. Lewis agrees and doesn't divulge any more details to Matthews.
While Michael puts Samantha to bed, Leila tells Sean that her father has given her an ultimatum: she must choose between Michael and Sean. Sean says he's not willing to part ways with Leila and he doesn't care what Michael or Sophia has to say about it. Leila tears up but not because she's moved; she tells Sean he hasn't touched her since he found out she wasn't entirely human. Sean apologizes and embraces Leila. He tells her to put off making any decisions until tomorrow.
Thomas and his men hold Sterling and Bell hostage. Thomas asks Sterling for the new code that will unlock the Inostranka gates. When Sterling refuses to answer, Thomas tortures him mercilessly. Maya witnesses the abuse and overhears Sterling talk about Thomas' cruel treatment towards Sophia's followers. Unable to witness Sterling's treatment, Bell tells Thomas the new code and unlocks the gates. Thomas exits but takes Sterling with him as he and the detainees board a helicopter. Before the helicopter takes off, Maya tells Sterling that Thomas does not represent the peaceful vision of her people. She urges Sterling to make a run for it. Thomas shoots at Sterling as he runs off and Maya courageously steps in front of the gunfire, saving Sterling's life as she loses her own.
The next morning Leila wakes up and realizes Sean is gone. It's unclear where he's going, but he's going alone. We see Sean walking down a road, looking miserable. The Matron from Willow Brook visits Dempsey in his luxurious study. She tells him that Leila and Sean were able to find and set free all of the "test subjects." A look of concern flashes across Dempsey's face. He walks to a strange board carved with intricate symbols. After making a mystical pronouncement that sometimes the past and the future blur together, Dempsey mysteriously tells the Matron that he has a feeling he'll be meeting Sean soon....