At this point, I'd like to address the issue of Leila's kidnapping. Why would they go to all the trouble of faking the list of passengers and putting stooges in the room but then let Sean run around free to cause trouble? Seems weird.
Okay, that was fun. Back to the desert. Michael, who looks like he might be dying, tells Sean he had no choice, and that the baddies were going to kill Leila. But Leila knew her captors. She called them "Vicki." The "Vicki" who was off snorkeling with Sean when Leila got snatched? See, that's what I'm talking about! If Vicki was part of the kidnapping plan, it seems like it would have been a good idea to grab Sean at the same time.
Black helicopters show up. That seems like a bad sign. You never hear someone shout "Hooray! The fleet of black helicopters are here!" Michael, still in "last words" mode, tells Sean he can't trust anyone and that he has to save Leila. Finally, we have a motivation. Get on that, Sean! Go! Go! Go! Go! You have to save her! Go! Sean runs off through the desert.
Back to Coral Gables, where people are still a bit bothered by the plane that vanished out of the sky. After everyone gets stuffed into their cars, we see the motorcade go back across that bridge that Simon Lee drove across last episode. In the Presidential Limo, President Martinez's son is worried that people were trying to kill them. That's a perfectly rational fear, but his father reassures him.
The motorcade arrives at the airport, which we just learned is an incredibly unsafe place. Michael hijacked a plane, Sean got on board with a gun, and Simon drove through the fence and right down the runway. You'd think they'd have some sort of law enforcement agents swarming all over the place by now. Or at least someone fixing that fence. Martinez tells someone to take his wife and child to an off-screen bunker, which is something I bet Jack Bauer wishes he'd thought of.
The scene now moves to a Situation Room of some sort, which is full of computer screens and technology. CIA Director Sterling, who was mysteriously absent for the press conference, reports that the co-pilot got a radio message off, saying the plane was going to crash into the retreat in Coral Gables. I don't think that matches up with what we saw happen, since the air traffic controllers never heard that message and we saw them all the way up until the radar went out. But that could easily be Sterling lying rather than a plot hole. Speaking of lying (nice segue!), the government will be telling people that the reason they thought they saw a plane disappear was some gibberish about a "mid-altitude marine layer." The President is more interested in talking about what actually happened to the plane. A general says that they haven't found the plane yet, but there was an off-the-charts blast of electromagnetic radiation. "The problem is, sir, we have no idea what this means." Nice work, general! Martinez asks, "Does out military have any weapon that could do this?" Nope. No one else does either. Director Sterling says that leaves only "one other group".