Prometheus made me seriously doubt the talent of Ridley Scott. It was so disjointed, and the horror aspects felt forced and boring.
But, basically, the idea is that there's this group of super-beings that goes around basically seeding planets with life. That's what the opening scene is. To create life, a super-being sacrifices itself so its DNA can seed life. Earth is one of those planets. Earth went off track. So, 2000 years ago, the super-beings send one of their own to Earth to get people on the right track again. The people of Earth seriously screwed up, which got these super-beings really angry and so they planned a super-weapon to wipe out life on Earth.
And so when the movie begins, the humans have discovered this super-weapon. They don't know it yet, of course.
Also, try and guess what happened 2000 years ago that might greatly offend a race of super-beings.