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This question is a little complicated but I will try to outline problem as neatly as possible.

In Alien, the crew of the Nostromo land on a planet, find what we would now know to be an Engineer ship, and inside that Engineer ship there are face-hugger eggs.

In Covenant, we see that the Engineers were wiped out by David when he arrived on the Engineers' home world, and he then set about developing the xenomorph life form.

Here's the problem though. The face-hugger eggs did not exist before the Engineers were wiped out. David worked for a long time after the extermination of the Engineers to create the face-hugger eggs. So how did a bunch of face-hugger eggs end up on an Engineer ship, wrecked on another planet?

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    Engineers probably exist on others planets, seeing as they were colonizers. Maybe someone with more knowledge can flesh out this comment? – BlueMoon93 Jun 19 '17 at 10:55
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    I believe Ridley Scott himself said somewhere that one of the reasons he came back to the franchise and made Prometheus (and later Covenant) was because he wanted to explain how the ship in Alien crashed and why it was carrying all those eggs, so this should all get explained in a future movie. – DisturbedNeo Jun 19 '17 at 11:21
  • "In Covenant, we see that the Engineers were wiped out" - we see how a certain (considerable) number of them is killed, but after all, it is a single city on a single planet. Is it even safe to say the planet is the home world of the Engineers, rather than just one of the worlds they lived on? – O. R. Mapper Jun 22 '17 at 20:36
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Yes, Alien Covenant is canon - but we don't yet know exactly how the two films will end up linking.

It's a simple answer, and not an all that satisfying one, but it's the truth. Alien: Covenant is set in 2104, but Alien takes place in 2121, a full 17 years or so later. Ridley Scott has said multiple times that there are still films yet to be made about David and his creations - I imagine that one of them would show us how the infected Engineer ended up on LV-426.

It's probably worth noting that the race David wiped out in Alien: Covenant probably aren't Engineers. Although they look similar, they're also significantly shorter than the Engineers we meet in Prometheus - it could be that they're another "creation" of the Engineers, much like humans.

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    I found your answer most satisfying. I had not considered the possibility that the species David wiped out may not have been Engineers. – Magikarp Master Jun 19 '17 at 11:26

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