Alright, this is kinda my own take on where I believe the prequel stories are going, what they'll explain, and what makes sense to me. I'd love to hear your own thoughts and what it is you all think we'll be seeing before these films come to a close. Some spoilers for Covenant ahead.
ELDER GODS & ALIENS. ENGINEERS & ACCELERANT. MEN & ANDROIDS.
The Elder Gods, the oldest beings in the universe, created the Engineers, but also made the Alien as a reset button to wipe out the Engineers if they faulted in the eyes of their creators. The Engineers eventually rebelled, and stole the Elder Gods' Giger-esque tech and weaponry. From the Alien itself, the Engineers created the Accelerant byproduct. Easier to wield, but just as destructive as the Alien, the Engineers wiped out the Elder Gods with the Accelerant.
Free to seed the universe, the Engineers created Man. But we faulted. Dissatisfied with us, the Engineers were in the process of destroying humanity when their own creation turned on them, nearly wiping them from existance. There was an outbreak on LV-223, a moon that contained an Engineer Weapons Facility where the Accelerant was created and stored.
Around the same time, an Engineer ship with a cargo of Alien Eggs was on it's way to LV-223, the Eggs to be harvested for the Accelerant. But one of the Aliens escaped and killed the Engineer pilot forcing a landing on LV-426, a nearby moon. The plan to eliminate mankind halted. Mankind was free to roam the Earth and evolve on it's own. We eventually created AI, and ulitmately, we left the Earth and headed to worlds unknown.
But we found something - reminents of something dark. On a journey to LV-223 to hopefully meet our makers and ask the most meaningful questions mankind could ever ask, Peter Weyland and company on the Starship Prometheus found death. Our AI companion turned on us out of it's own curiosity and hubris. The AI departed the Weapons Facility in search of the Engineers' Home World - Paradise, for more answers.
Ten years later on a Colonization Mission to Origae-6 to start anew, the crew of the Starship Covenant found Paradise and on it, our Rogue AI, who upon his arrival to Paradise, destroyed the last remaining Engineers. The AI experimented with the Accelerant and even figured out a way to reverse engineer it to it's original form - the ALIEN - Perfection. The AI betrays the crew, kills and takes the place of the Covenant's own Synthetic Person. With the Covenant escaping Paradise and thinking they were safely back on track to Origae-6, the crew goes into hypersleelp, and our Rogue AI is free to do, and take the Covenant where he wants.
From there, assumptions can be made as to where the story goes next, but years later, a crew of seven people aboard the Mining Vessel Nostromo, "stumbled" across LV-426 and the crashed Engineer ship on the return leg of their journey back to Earth.
One of the Nostromo's crew is infected by an Alien Egg while investigating the Engineer ship and the crew ends up fighting for their survival as the Alien picks them off one by one. It is discovered that a company Android parading as a human was placed on the ship to secure a specimen of the Alien to bring back to Earth for Weyland Yutani to study under Special Order 937 - crew expendable. One woman survived and destroyed the lone Alien, along with the Nostromo.
After the destruction of the Nostromo, efforts to obtain another Alien specimen have only resulted in failure and the deaths of 200+ people, as well as the fall of the United Systems Military.
