As Sean and the FBI are getting ready to leave the scene of the plane crash, they're hit by an RV for some reason. Sean pulls the female agent from the car but everyone else involves is smooshed dead and then lit on fire. When don't Hollywood car crashes end in explosions?
While the FBI agent was unconscious, Sean got into her computer and downloaded a picture of the chick who kidnapped Leila onto it. He wants the FBI to run facial recognition software on it to find out who this chick is. In order to do that, he hides out in her trunk and sneaks into the FBI server room. Suuuuuuure. Aliens, I'll believe. Easily sneaking into the FBI and hacking into their facial recognition program? No.
The Chick Sean Wants To Facially Recognize is driving with Leila in the back of a Rape Van when she's pulled over by a cop, whom she promptly kills. In the meantime, she's in the FBI system under multiple aliases.
President Underwood heads to the site of the plane crash landing, seeing all of the passengers scattered across the desert. He then heads to see Sophia, to confront her about the existence of the other aliens, and his suspicion that they're the ones responsible for the deaths of the passengers. She won't snitch. He's all, Whatever, bitch, I just told everyone up at that Alaskan prison that I'll free whoever gives me the info I want.
And sure enough, someone takes him up on his offer. The Alien Dude meets with the Director of National Intelligence, but demands to get his girlfriend out of the prison too before he'll give up the details. So his girlfriend is released.... and promptly kills him. Sophia had asked that the Alien Dude be "dealt with harshly" and I guess his GF doesn't take kindly to tattletales.
U.S. Intelligence is beyond intelligent, figuring out who Sean is and that he may have a role in the crash. They connect those dots REALLY fast. Agents from "the Washington field office" come to transfer Sean, but they're not really the good guys (they work for the Kidnapping Bitch), there's a shootout, and Sean and the Female FBI Agent drive off.
In the end, at the temporary morgue for the crash victims, the passengers start to sit up, coming back to life. ZOMBIES!?!? That's kind of cool.