Like so many aspects of FFXIII at present, what is known about the prologue and story is very vague, and makes very little sense. Here's us trying to put it together.

Square Enix has said very little about the story or Final Fantasy XIII so far, but they've managed to throw us a couple nice tidbits about the prologue to the story, as well as it's themes; determination, fantasy and futurism.
There are two known parts of the world of FFXIII so far, Cocoon and Pulse. Pulse, the planet, or at least a large part of the planet, is a land of wild monsters, and not much civilization, but it is there. Cocoon is a city in the sky, a perfect environment for humans to live in, protected by a powerful crystal. Beings themselves, crystals have specific motives and plans, Cocoon's crystal in particular is practically raising humans.

The citizens and holy government are very suspect of anyone in Cocoon who has been, or is believed to be, influenced in any way by the people of Pulse, and are banished from Cocoon.
Pulse also is said to have it's own guiding crystal. A symbol of peace, Pulse's crystal chose it's people, and determined their destiny to lead the world. Lightning was chosen as an enemy of humankind that will bring destruction to the world. Not much sense can be made from this, but since Lightning is seen invading Cocoon in the trailers, it wouldn't be crazy to think by humanity, they mean the people of Cocoon, but it is too tough to call.

Final Fantasy XIII starts off with Pulse being pretty fed up with the society of Cocoon, as they plan and carry out an assault against Cocoon. Lightning leads the charge of the assault, as it's said to start a quasi-revolution. Cocoons strength as a fortress are supposedly susceptible to infiltration, which frightens the people of Cocoon. They fear the possibility of the City falling from the sky.