The Engineers are time travelers. In the beginning of the movie - we see them go back in time to plant the seeds of life on an infant planet Earth - using their own DNA. The purpose of this is left for us to determine. Maybe they just travel the universe building worlds.
Then they discover that they F'ed up because we humans end up screwing up the universe in some catastrophic way - so they now need to undo this mistake. Barring the Back to the Future concept of time travel where they can just go back to a time before they created humans and prevent that event from happenning - they realize that they have to try to eradicate humans from all possible timelines. This was my gf's concept - I'm not 100% on board with it. The idea is that the one act of creating life on Earth creates a multitude of other possible futures that now each have humans that need to be eradicated.
So that is why there are multiple ships with the Alien spore? cargo in them. Like a massive temporal genocide campaign. One of those ships is the ship that the crew from "Alien" happen upon in the timeline that is the setting of that movie. Which is why Ridley insists this movie isn't a prequel to the events of that movie - because it exists in a completely different reality.
To me - the whole setup in the Space Jockey chamber always looked like it served more than just simple navigation through space. So maybe time travel isn't so outlandish. Would also explain why their bodies are so well preserved.
Then we speculated that maybe in the next movie - Shaw and David discover exactly what it is that humans did to f up the universe and deserve extinction.
Anyways. That's what my old lady and I came up with over a couple glasses of wine.
