Warning: The following contains spoilers for Alien: Covenant.
Prometheus co-writer Damon Lindelof has some ideas about where the sequel to Alien: Covenant will go. Covenant seemed to settle the fate of the Engineers, the race of God-like beings introduced in Prometheus, when a flashback sequence shows David bombing them with black goo, turning them into lifeless statues. After seemingly wiping out the Engineers, David begins his own experiments in manufacturing life - experiments that lead eventually to him creating the classic Alien Xenomorph. The movie ends with David taking control of the Covenant and its hundreds of hibernating humans, plus Daniels and Tennessee and a couple of Xenomorph embryos, and resuming the mission to the Covenant's original intended destination of Origae-6.
The ending of Covenant seems to suggest a road for a sequel that involves David creating a whole race of Xenomorphs using his two embryos and his hundreds of helpless potential hosts, with no further role for the Engineers (who were presumably all wiped out by David anyway). But at least one person with knowledge of Ridley Scott's thought-process thinks we shouldn't be too hasty in writing off the Engineers as continuing players in the Alien universe.
Lindelof spoke to Collider about Alien: Covenant and advanced a theory about a potential sequel that would have the Engineers coming back into the picture. Lindelof talked about his and Ridley Scott's thought-process in writing Prometheus and some rough ideas Scott gave him about where he wanted to take the series:
“I think that one of the conversations that we had at the end of Prometheus is, Shaw and David have basically locked in on the coordinates of the planet where the Engineers came from. What does that place look like? Ridley called it ‘Paradise’. What happens when they land on that planet? It doesn’t feel like they’ve gotten there yet in Covenant, Covenant felt like it maybe was a detour prior to them arriving at the place of origin so I don’t want to spoil any place that he might still be wanting to go, but the conversations that he and I had about where the story goes next were largely about the place where the Engineers were from and less the events of Covenant.”
In Alien: Covenant, the colonists end up on "Paradise" after a neutrino storm wreaks havoc on the ship (killing James Franco in the process), and the prematurely-awakened crew decide to detour to this other nearer planet after receiving a seeming distress signal in the form of a John Denver song. When they arrive on the planet and discover David, they and we are led to believe that this was the Engineers' home-world and that David wiped out all the Engineers, but Lindelof is saying what if "Paradise" wasn't the Engineers' home-world but was merely an outpost? What if the original destination of the Covenant, Origae-6, is the actual Engineers' home-world and now David is heading there with his cargo of hosts and Xenomorph embryos?
Lindelof's theory would actually help boost the plausibility of what transpires with David and the Engineers in Alien: Covenant. As many have pointed out, it doesn't make a ton of sense that a race as powerful as the Engineers could so easily be exterminated, but perhaps David only killed a small number of the Engineers at one remote outpost where they were somewhat vulnerable. The way the Engineers behave in the flashback - all standing there in awe of the single ship hovering over their city - makes somewhat more sense if this is an outpost and they were not expecting this ship to show up.
All this theorizing could of course be moot, considering the alarmingly low box office returns for Alien: Covenant and the uncertainty surrounding the future of the franchise. Ridley Scott may have big, ambitious, cool plans for more Alien movies, but he may never get a chance to realize those plans.