Simon's pal has found the container that brought the isotopes from the armory to the coffee shop. They have two partial prints, which should be enough to identify the mole.
Sean and Leila run through a parking lot and down a street. Leila wants to know where they're going, and I think the correct answer is "Away from those goons with the automatic weapons." She stops running, because she is dumb. Sean tells her he's going to untangle this whole thing so they can get back to living their lives. He insists that they're going to be okay, which I have a hard time believing. A good start would be for them to stop having this conversation out in the middle of a street.
Hospital. Simon wakes up, and Sterling is watching him. He tells Simon that they tested his blood and DNA, and Simon plays dumb. Luckily, the blood came up Human. And the prints from the vial matched Murphy, so they've decided he's the mole. We see Aaron (wearing an FBI badge) stroll into the coffee shop (which is under quarantine) and flagrantly transfer some prints onto it.
As Sterling looks on, agents arrest Murphy. Even though he was in the situation room when the isotopes were planted in the coffee shop. I guess they think he stole the isotopes, ran to the coffee shop, dosed the milk jug, ran back to the situation room, told Sterling that someone had stolen the isotopes, volunteered to find the traitor, punched himself in the face, and locked himself in the trunk.
Thomas tells Sophia that Simon will be fine. He also calls Sophia "Mother," which may or may not be interesting. Sophia wants to know how far along Thomas is on getting everyone home. He babbles about Cesium isotopes and claims that he's gotten the American nuclear capability to the point where he can open portals, but he doesn't have enough raw materials to go home. So he needs some nuclear warheads, which are allegedly full of raw materials. Here's an interesting fact: nuclear warheads are actually full of highly processed and refined materials, assembled in a precise configuration. You can't just grab a handful of raw plutonium and stuff it into a nuclear warhead.
At home, the president watches a news report. It claims that the passengers of Avias Air 514 are doing well. There's no word on the current cover story, which you'll remember began with a "mid-Atlantic weather pattern" to explain a jet vanishing in full view of thousands of people (including a bunch of news reporters with cameras) and later involved people losing track of the plane over Brazil or someplace. Sterling enters to report on the mole situation, which in his opinion is that Murphy was the mole and they caught him. They're presumably waterboarding him right now. Or possibly strapping him to a ducking stool. Or using any of a number of medieval tortures that would be appropriate in this situation. Sterling apologizes for having been wrong about Murphy, and you know he means it because of that time with Laura in the flashbacks. Martinez offers Sterling a beer, and Sterling accepts. Then Martinez just pours out a glass from the bottle of beer he was drinking, which seems kind of cheap. Give the man a whole bottle, Prez!