The game was awsome!
I love exploration games like this, which have a bit of puzzle solving.

This one didn't require you to babysit the rather annoying ball, either.

On the downside, the ending sucks!

*spoilers*


Seriously, I abhor cliff hangers....
The ending is basically just you are forced into stasis and the remnants of humanity are now lab rats.

In addition, I get that the aliens were doing some sort of experiment, but it's never made clear what the experiment is!
What's actually going on there?

***BIG SPOILER BELOW - BIG SPOILER BELOW ***

I agree that this game is awesome. Personally I loved the ending, especially in that it suggests a sequel. Not every ending has to be happy & 100% conclusive, indeed I think it's often the best endings that aren't.

Anyway, on to your question. The full explanation is scattered over the documentation you can read throughout the game and I guess it's easy to miss key parts. The impression I got is basically this:

There was some kind of ancient, advanced race in the galaxy long ago. The 'baddy' aliens of the game found an orb left behind by these 'ancients', an orb which could provide an endless supply of energy/power. For some reason the 'ancients' encoded the key to unlocking this power into humanoid DNA (suggesting that they were also responsible for creating/seeding humanoid life). Therefore the bad aliens began to search for these humanoid lifeforms on different planets in order to harvest and study their DNA and piece together the key. They haven't studied humans yet, so they used the 'hero' of the story to lure the last of humanity to the planet to set up a colony. (There is also mention of DNA purity and that they are looking for particularly pure sources of the original DNA).

The game leaves us with the hero captured by the aliens and the last humans presumably beginning their long voyage to the planet. Can the hero escape? Will a third party intervene to rescue him/her? Can the hero then do something about the aliens before the remnants of humanity arrive? Maybe the 'ancients' intended the key to their power to be found by their humanoid legacy (why else encode it in their DNA?) and perhaps they are still out their somewhere.... :)

Brilliant game and I really hope we get more (though with more originality e.g. less copied from Lost).

p.s. smoke monster aside, did anyone else notice that the opening scene with fiery debris raining from the sky echoes the opening scene from Lost with the burning aircraft debris falling into the sea?