My prediction for the first level.
The planet Master Chief lands on is an unknown and mysterious installation in which a UNSC fleet, and an Elite fleet has been sucked into (separately at different times).
Master Chief recovers from the Frigate crashing on the planet, and comes out to see a mountainous, grassland environment. Cortana states that she has no idea where they are.
Chief either carries an MA5C out with him, or a prototype Assault Rifle (which will be the AR in the game), and heads off to scout this new location.
After running around the area, (going through control tests and trials), I think a cutscene will occur in which either Cortana says she's reading movement, or Chief sees something.
In the cutscene, Chief tracks down whatever was stalking him (the new enemy which I won't attempt to identify) to find it, where upon he is attacked by it. He kills the thing, and Cortana warns that there are more coming.
For the rest of the level, you're trying to make your way through the area without being killed. Along the way, you see a lot of Forerunner structures, which Cortana comments on, and my guess is that there will be a few clues as to the whereabouts of the plot.
At the end of the level, Cortana is shocked to the fact that she is receiving a human voice on the comm.
In the very last firefight, a Pelican dropship seemingly appearing out of nowhere arrives and deploys fresh troops to take out the hostiles attacking Chief.
The UNSC is surprised to find the Master Chief, and Cortana.
As to actual plot, I'm going with what Cobra said, mostly. Going with his theory, I'm convinced that the Forerunners might have absorbed as many ships that happened to pass by as possible to fight either an entire faction, or an overlord and his force supposedly.
But Halo is not Halo without the plot making a sudden turn. I also believe that at some point in the game, we'll either come face-to-face with an new, reformed Covenant brought about by completely different means than the past Covenant, or a completely separate Covenant-like faction that heavily influences where the story goes.
How'd they get there? If the planet is sucking ships in at random in hopes of desperately finding a hero, then perhaps the planet also sucked in those guys as well.
I also believe that halfway through the game, Forerunners will appear at the scene to assist you through the remainder of the game. I don't want to go into all that would happen and be revealed during that time.
Also, the Flood is going to be in too, but they're most likely already on the planet somewhere.
Also, I don't believe the entire trilogy is going to be founded on one central idea, but rather, the way the first one went with it all taking multiple twists and turns.
[Edited on 09.07.2011 3:46 PM PDT]