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Since I couldn't post a spoiler as the question itself, I'll clarify what I mean here:

The movies ‘Alien vs. Predator’ and ‘Aliens vs. Predator: Requiem’ take place in 2004, a hundred years prior to ‘Prometheus’ and ‘Alien: Covenant’, and the temple with the xenomorph eggs found in AVP has seemingly been around for thousands of years.

Yet in ‘Alien: Covenant’, which takes place in 2104,

the character David is shown to have genetically engineered the xenomorph after wiping out life on the planet with the Engineers' own weapons. So what happened here? Are AVP/AVP: Requiem no longer canon? Or did the Engineers previously create something almost identical to what David later created, and we’ll somehow see that in the unnamed third movie in the Prometheus trilogy?

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    Sigh. The more backstory they give the aliens, the worse the series seems to become. – Valorum May 20 '17 at 5:49
  • Don't forget the possibility of time travel. Maybe the eggs found in AVP had come "back from the future" as a contingency plan, such as might be found in an episode of "Doctor Who"? – Lorendiac May 20 '17 at 14:59
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    @Valorum I concur. In fairness, though, this seems to happen with ALL horror franchises eventually. The first one (or two) are amazing, and after that they begin to disintegrate... Personally I think the lack of known backstory is part of what makes any given movie monster scary, so it's kind of inevitable in that regard. – Steve-O May 21 '17 at 22:36
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The Alien versus Predator movies are not in the same canon as the main Alien movies. Prometheus already showed signs of it:

Yet accompanying the release of 2012's Prometheus, Sir Ridley Scott's long-awaited return to the Alien franchise, the promotional website Weyland Industries retconned the AvP movies from the canon by having Peter Weyland as the founder of Weyland Corp, as opposed to having AVP's Charles Bishop Weyland as the founder of Weyland Industries.

Fox to make Alien vs Predator movies canon?

Yes the article further mentions that a new teaser website has small bits of Predator in there. But I'd put those as small easter eggs or hint of a new movie. In any case, Prometheus is directly in contradiction with Alien versus Predator.

So, the answer as shown in Covenant is:

David created the xenomorph.

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To use an analogy: Suppose I made some homemade wine. I'd research the method for wine-making, buy some equipment, use some ingredients and make wine. The process would be similar to one from thousands of years ago, but with some variations. Just because I made some bottles of homemade wine last Summer, it would be a fallacy to claim that all wine was made by me, or that I invented it. Right? I mean, what about those ancient Roman wine amphorae that have been discovered in shipwrecks? Did I somehow invent that wine as well? That line of reasoning make no sense whatsoever.

So why do so many people keep applying that faulty logic to David and the Xenomorphs, by assuming that because he made a Xenomorph he made all of them, and invented them?

Consider the following:

  • In Prometheus, creatures similar to the Xenomorph were depicted in the mural
  • The 'Deacon' has a similar morphology to the Xenomorph
  • In the Prologue, "The Crossing", David made reference to studying the ways of the Engineers while en route to the Engineers' planet
  • At no point in the film did David say anything about the eggs or facehuggers being an original creation of his
  • In Alien, there's an Engineer ship full of the eggs. We don't know how it got there. It may or may not be a truly ancient derelict, we don't know
  • In the Official Movie Novelisation for Alien: Covenant, David says of the eggs in his Lab:

Oh, Captain.” David shook his head sadly. “Acknowledge beauty when you see it. Even if its appearance disturbs you, surely you can admire the skill that went into its design. In case you are wondering, I had nothing to do with it. It lies as I found it, a supreme example of the Engineers’ skill. And also, I suppose, of their hubris.

Would that I could create something so perfect in its function,

Alien: Covenant - The Official Movie Novelization

The black goo mutagen is a highly chaotic substance, as demonstrated in Prometheus and Alien: Covenant. The possibilities and potential of this stuff, and the rest of the Engineer's tech, means that the numbers of variations of weird mutations and creatures, their variations and the way they and their lifecycles adapt, is far vaster and more complex than we expected from Alien, i.e. facehugger > chestburster > Xenomorph.

We've already seen that in almost every Alien film there's a slightly different lifecycle, variation of alien creature etc. as well.

What Ridley Scott has done with Prometheus and Alien: Covenant is reveal an alien technology that serves the narrative purpose of vastly expanding the lore to include all kinds of possible horrors. The question about the origins of the creature we see in Alien is deliberately left ambiguous in Alien: Covenant. Nothing in the films confirms or denies that David invented the Xenomorph we saw in Alien, and it would be a fallacy to assume he did.

What we do know is that the Xenomorph depicted in Alien is just one possible result of some kind of engineering work. Maybe it's an Engineer bioweapon, possibly as a result of an accident involving black goo and a biomechanical entity of some kind, possibly engineered thousands of years ago, possibly cobbled together by David from experimentation aboard the covenant. There is simply not enough information in either films Prometheus or Covenant to conclusively say.

The novel says 'no', however, and that's the closest to a definitive statement we have.

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    "In the novel"... In which novel? – Valorum Oct 10 '18 at 20:51
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    "Alien: Covenant: The Official Movie Novelisation" by Alan Dean Foster. My apologies, I assumed it would be clear from the context. – dogsolitude_uk Oct 11 '18 at 7:14

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