The Event/WMG

The aliens were surveyors looking for a new home planet.
Barely a WMG since this is clearly what all the hints are leading toward, but this is the best place to put it. Their home planet is stated to be nearly dead, therefore they need a new one. Sophia's objectives seem to be dealing with the humans as little as possible so as not to corrupt us according to her version of the Prime Directive and getting her people out of here, but some have decided to integrate and Thomas wants to kill us all and take the planet. The question is, why did they come 75 million light years to find a new home?
 * Pretty much confirmed.

Sean is a CIA operative.
Michael seemed to trust Sean for a reason he wouldn't explain; this one is as good as any.

The Event is when everyone stops watching "The Event".
It's so scary and mysterious and everyone seems to want to prevent it.

The Event is The Event.
THE EVENT!

The captives can distort time.
That's why we see everything in anachronological order!

The captives are perfectly normal, but the government thinks they're screwed up.
Now that's what I call a conspiracy.

The Event won't involve aliens, psychics, alternate dimensions, super powers, or time travel.
Instead it will involve Cthulhu, fairies, or a floating island of Dinosaurs that is pissed off at how we're destroying the planet. Other serials have already used super powers, aliens, time travel, etc. If they turn out to be 'the event' the audience will have been there and done that.
 * Alternatively, the Event will involve time traveling alien psychics with super powers from an alternate dimension.

Greg and Vicky, the couple Sean and Leila met on the cruise, are secret agents of... whatever the whole conspiracy turns out to be.
Leila disappeared right after meeting them, and so far they have no apparent purpose on the show.
 * Confirmed in the second episode. Vicky is certainly a secret agent for the conspiracy to take down the plane (which probably isn't the only conspiracy in play). Greg was, until he made too much trouble.
 * Was he in on it? My impression was that he was just a dupe Vicki picked up somewhere as cover.

Sean is actually brainwashed or somehow evil.
Michael was trying to crash the plane to destroy him for the greater good. Possibly he was also trying to kill Sophia, who was at the site the plane nearly hit.

Sean is an alien sleeper agent.
He had his mind wiped so he could pass as a normal human. This is why so much of the plot revolves around him. There may be other sleeper agents in the cast.
 * Or he is only half-alien. He got an IV-drip, but aliens apparently don't have a major vein in their arms.
 * Alternatively...

Leila is the evil mastermind!
OK, so this one was all but Jossed once we actually saw her being held captive, but this is on my personal list of Twists Awesomer Than The Ones The Show Actually Went With.

Vikki and her cohorts are Fantastic Racists.
They got Michael to crash the plane to kill Sophia, or at least put doubt in the president's mind. They need to get rid of Sean because he's the only person who could clear the name of the aliens.

There are no bad guys, except the paranoid bastards - both human and alien - who insist that the other guys are bad guys.
The aliens arrived in 1944, at the height of World War 2 - the Axis were shoving all the "inferior races" into concentration camps, the Allies were shoving Japanese into concentration camps, and then they themselves were shoved into a concentration camp. Only an idiot would trust someone who's shoved them into a concentration camp, so they keep their mouths shut to protect the ones who escaped. And the government keeps getting more and more paranoid because these uppity aliens won't bend over the way good citizens do, and the aliens keep getting more and more paranoid because the government is becoming more and more repressive. "The Ev3nt" is when all that paranoia finally escalates into war.
 * Oh, and it was the DCI who arranged for the attack to keep the President from revealing the existence of the aliens, and the aliens who averted it in the hopes of preventing another War On Terror - only now the President has been infected with paranoia and is ordering a witch hunt. IT IS GOING TO GET WORSE.

The event does not actually happen.

 * I believe that the Event will happen, until one tiny minute detail goes wrong and The Event does not happen, but then they go on the TARDIS (Or whatever the hell the plane's s'pposed to be) And go Back to the Future whereas then they change so the event happens but because they changed the original event goes horrendously wrong, and The president kills them all beforehand. Discuss.

Dempsey is the Devil and the "aliens" are actually Fallen Angels trying to get back into Heaven
Based on his transformation in the mirror into a, younger self at the end of "For the Good of the Country". Which would make the Event the Apocalypse. Alternately...

Sophia has slight-mind control abilities over her people.
Sophia managed to get Isabelle to confess almost immediately, and Isabelle would, under normal circumstances, probably try to deny everything. But instead she does everything Sophia says, albeit tearfully. It could be genetic, with Thomas and Sophia being a Queen-type caste of the species, and Thomas has similar abilities (although Sophia's are more powerful). Isabelle said that if Thomas killed Sophia, the aliens would follow him, but they do still admire Sophia as a leader no matter what.

Martinez is a functioning psychopath.
Notice how quickly he shifted from "reasonable" to homicidal, and continuously cuts off any attempts at negotiation or explanation, something a person trained in negotiation would never do. As soon as he realizes Sophia has no leverage, he goes straight for the mass murder button When Dempsey is the voice of restraint, you know there's a problem. Martinez's President Personable act is just a front for someone who's essentially Dexter without a code.

The Inostranka raid 2-hour episode was probably meant to be the original season finale.
In addition, the  may well have been intended as the second season finale.The production values and nonstop action of the Inostranka raid is just the kind of thing that seems like it would be in a season finale, with a big event (the turning of Thomas against Sophia and the freeing of the detainees) as the big cliffhanger of the season. Because the series is obviously nearing cancellation and thus the writers are being forced to Wrap It Up to make the first (and only) season finale an appropriate Grand Finale that ties up everything, they were forced to rush through everything, cutting out many of the flashbacks and putting the Inostranka raid in the middle of the season instead. Afterwards, there probably would've been more flashbacks about Thomas' early time on Earth, his motivations, etc., as he became the second season's major villain. Meanwhile, Sean and Vicky would have much longer to bond on their journey to France and their relationship would be quite intense by the time they finally reached Dempsey's lair in the Jura Mountains (probably they get caught and captured and that's the second season cliffhanger), while the season itself would've ended with  and Sophia's reaction.

Sophia's people and Martinez will eventually be forced to put aside their differences to take down Dempsey.
Watch how Dempsey is currently messing around with some kind of ancient ruin. He's obviously after more than just eternal youth or money, he seems to want some kind of power seeing as how he tried to kill the president (and Sophia, though she wasn't his target at the time). He's likely the person Thomas was referring to when he was telling Sophia just why humans are such monsters, Thomas probably stumbled on one of the half-alien girls who Dempsey drained of youth and this may have been the last straw to set him against the human race. Eventually, Dempsey is going to become enough of a threat to force Sophia and Martinez to put aside their feud and unite to stop whatever plans he's cooked up. Dempsey will end up as the Big Bad of the whole series.

Using Leila to mutate the disease will come back to bite Sophia in the ass
It will mutate but to a form that effects Sophia's people as well as humans.

The aliens are humans who left Earth thousands of years ago.

 * The way things are going, this will probably be either debunked or confirmed in the next episode.

Sophia will sacrifice herself to stop the virus but her people will still get to Earth.

 * Sophia, feeling remorse for what she's done, will make a deal with the president to stop the virus, asking only that her people are treated well upon their arrival on Earth. Stopping the virus will involve her sacrificing her life.