In myth, Prometheus makes man from clay, sides with the gods against the titans, and steals fire from the gods and gives it to man, only to be condemned for it. So, I suppose the "Prometheus" we see at the beginning of the film is part of one faction of engineers that creates and guides human life, against the will or law of their race, while the ones we see at the end of the film are part of another faction seeking to destroy their works. Their enemies. If the "good engineers" gave us fire, that is technology 2000 years ago, perhaps the "evil engineers" are out to destroy the perceived threat of us. Or maybe to them, all or them, Earth was just a petri dish that served its purpose, and now goes to decon.
Just a guess.
Oh, and A-. It was great.
That is a reasonable explanation. And I agree this is the best sci-fi flick IMO since Trek XI.
Regarding box office totals the film brought in $50 million in the US
And, worldwide its brought in $141 million
It cost Fox and estimated $130 million
to make the film and as pointed out 1/2 the cost The Avengers
However, Avengers is up to over $1 billion in box office receipts worldwide so at this point Prometheus has just barely paid for itself.