Warning: Major SPOILERS for Alien: Covenant ahead
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Though Ridley Scott's Prometheus shared a lot of imagery and theme with its forebears, the additions it made to the overall canon of the Alien series left many fans with more questions than answers. Who were the Engineers, really? How did the xenomorphs go from being smaller, white creatures to the jet-black Giger-inspired nightmares we commonly know them as? And what the hell is the story with that black goo? The film itself was middling at best and the presiding worry afterwards was that whatever history Scott had come up with to lead into Alien, he'd already written himself into a corner he'd struggle to get out of.
Thankfully, Alien: Covenant does provide some answers, for both Prometheus and Alien. As a near-direct sequel to Prometheus and an indirect prequel to Alien, Covenant's story is filled with information on what exactly happened in Prometheus, the nature of the Engineers and how the xenomorphs came to be. Covenant still has its fair share of loose ends by the time the credits roll, but its connections and implications on the Alien mythos are made clear from the get-go and wind up running quite broad by the end, for better or worse.
Engineer Homeworld
Much of Alien: Covenant takes place on the planet David (Michael Fassbender) and Dr. Elizabeth Shaw (Noomi Rapace) were travelling to at the end of Prometheus, believed to the Engineer homeworld. After receiving a human distress signal from the planet, the crew of the Covenant decide to check it out as a possible alternative for their colonization mission since their actual target is a much greater distance away. Tracking the source of the distress beacon, the team discover the Engineer's ship David and Dr. Shaw used, now abandoned and overgrown with plant-life having crashed onto the planet's surface. They find Shaw's dog-tags, but other than that the ship is void of life.
Two crew members become infected with airborne spores during the expedition and, after a period of rapid illness, both have neomorphs rip out of their bodies – proto-xenomorphs similar to the one seen at the end of Prometheus. The ensuing chaos leads to the arrival of David, who brings the surviving crew to a large stone temple surrounded by an expansive courtyard littered with bodies coated in a black substance. David reveals this is where he's hidden out since he and Shaw landed, initially lying about what happened to Shaw on the Prometheus mission.
David explains that the spores that have been infecting people and creating aliens are a result of a bio-weapon the Engineers manufactured to wipe out all living things on a planet. On LV-223 they lost control of the substance, leading to the events of Prometheus. After journeying to the Engineer planet the Engineer ship, David released a canister of the chemical onto the surface, starting a chain reaction that began with all the bodies seen in the courtyard and ended with the ecosystem becoming mutated. Plant-life now stores the mutagen in spore-form, squirting bursts of it into the air upon being disturbed.
Xenomorph Origins
The crux of Covenant's addition to the Alien legacy comes in an explanation, or at least a hypothesis, on how the xenomorphs were created. David explains to his fellow android Walter (Michael Fassbender) and Captain Oram (Billy Crudup), the Covenant's captain, that he's been engaging in experiments of his own on the biological weaponry the Engineers were trying to cultivate. David is driven by the work of Peter Weyland, the two of whom we see at the start of the film talking just after David's activation about the search for greater forms of life and an obsession with discovering where the human race came from.
In Covenant it's revealed that David was using Shaw as a subject since she was infected with the mutagen through sexual inter-course to experiment with the chemical and living tissue, His goal was understanding the proto-/neo-morphs and move beyond them to a newer evolution, one beyond that of human beings and AI. Shaw died during these experiments, and upon discovery of her body on a table in David's lab, it's implied she suffered a great deal in his mission to create new life.
But David's work as a space Dr. Frankenstein yielded results, as evidenced by the skulls of small aliens and designs that show the face-huggers, alien eggs and xenomorphs in his lab - and the actual alien eggs and facehuggers he shows poor Capt. Oram before Oram is face-hugged and impregnated by one. Oram soon gives birth to a more conventional chestburster, except it has limbs as soon as it's born. This chestburster grows into the xenomorph that's much closer to that of Alien and Aliens, as seen in the Alien: Covenant trailers.
In the meantime, David and Walter have a fight that David wins with him taking Walter's place on the Covenant, unbeknownst to the surviving crew-members. After they re-enter cryo-sleep, David leaves an entry on the ship's log erasing the events of their detour and places two facehugger embryos in cryo-storage.
The big takeaway is that the xenomorphs were created by merging a chemical mutagen bio-weapon with living tissue to make an organism that multiplies itself through parasitic impregnation. As of the end of Covenant, it would appear that David has created the xenomorphs himself, but with how little that fits the established logic of the Alien movies (the fossilized, chestbursted space-jockey, for one thing) it's also likely Ridley Scott may have another idea in mind.
Scott has made it clear he has multiple films planned to make a prequel series. Looking at Covenant and Prometheus and their growing-but-still-insubstantive connection to 1979's Alien, it would appear he has a grand narrative in mind. Whether the obvious turns out to be true or something else, like perhaps xenomorphs already existed and David has managed to separately recreate them using the same ingredients, at the very least Alien: Covenant provided more answers for fans to chew on than its predecessor.