The question that was asked in Prometheus....'why do the engineers want to kill humanity' is answered. Kinda spoilers here:

Engineers create humanity. Humans build AI to find their creators. Ironically, human built AI is what threatens to kill our creators. So our creators create a pathogen to destroy us in order to protect themselves from our AI. But our AI gets ahold of their pathogen and uses it against them...and then develops it to be even more effective (the creation of the Alien) in order to kill off humanity. It's kinda poetic that the AI we made to find our creators ends up killing them. And it's a cycle because the AI we make, in turn, make the Alien which is destined to kill us. The engineers are to us as we are to AI as AI is to the Alien.

I 'think' I'm getting that right. In anycase....I thought it was great.