Those lucky enough to be at Fox's CinemaCon panel were treated to new footage from Alien: Covenant this week and The Wrap's breakdown of that reveals more on how the movie ties into the events of Prometheus. Apparently, the ship the duo took off in at the end of that prequel did indeed make it to the homeworld of the Engineers, but what happened next? Well, we may finally have an answer!
In the scene shown, it's greeted by hundreds of the Engineers and they watch on as David - who once again has a body - emerges from the ship and watches them all die before him as, "the ship unspools black bombs that cover the entire civilization in a black ooze that ends their bodies." That's presumably what leads to an infestation of Xenomorphs and a voiceover seemingly confirms that David will be portrayed as the lead villain when he looks to use those monsters to destroy humanity.
"The gods have rejected mankind as cruel, weak and full of greed. They are a dying species, grasping for resurrection. So they are leaving the Earth forever. But their power is an illusion. They don’t deserve to start again, and I’m not going to let them."
This is certainly pretty unexpected and still leaves us with a lot of questions. Whether or not Alien: Covenant is going to answer those is another matter, but based on Prometheus, don't count on it!