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At then end of Prometheus,

after the "Engineer" was attacked by the huge "face-hugger"

I had expected the Engineer to go back to his ship and sit in that large chair he previously used when attempting to leave the planet. I assumed this because in Alien the crew of the Nostromo found

the "Space Jockey" in a similar ship with his chest cage exploded from the inside, obviously killed by an alien "hatching" (or whatever you call it).

Isn't the crashed alien ship the same ship that the crew of the Nostromo found? If so, then where is the Space Jockey?

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No, they are not the same Engineers. The film Prometheus almost entirely takes place on LV-223. The film Alien (and Aliens, for that matter), takes place on LV-426.

We are to infer that a similar fate as what happened to the Engineer at the end of Prometheus befell the crew of the ship in Alien.

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    Thanks! Did not realize it was not the same planet.
    – knightscharge
    Jun 25 '12 at 18:26
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    Prometheus seems pretty well set up for a sequel, and I suspect that the story is going to be that the Engineers were essentially hoist by their own petard across the board, and wiped out by the weapons they intended to use to wipe out their progeny, i.e., us.
    – Chris B. Behrens
    Jun 25 '12 at 19:41
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    Fascinating. I had always assumed this had been a case of executive meddling, where the original intention had indeed been for the last engineer scene to lead up directly to what the Nostromo crew would discover. If the planet is explicitly said to be a different one throughout the movie, that sounds convincing for the two being indeed different. It also reduces the need for some suspension of disbelief, as the sets in the alien ship looked similar, but different in many details, so we can simply assume they were indeed two different ship types :-)
    – O. R. Mapper
    Jul 17 '14 at 7:18
  • We still need an explanation for the large cave underneath the Labia-adorned Horshoe Artifact from "Alien" (other than Bigger on the Inside. Did anyone notice that the Basestar Interior of Battlestar Galactica The Reboot seems to have been modeled after The Cave. Maybe it's been Cylons all along?
    – David Tonhofer
    May 2 '20 at 11:28
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The chronological order of the alien movies suggests that Prometheus comes first and then Alien: Covenant. It could be the same ship or it could be a similar one. However, with Prometheus and Alien: Covenant being considered prequels to the other Alien movies, this suggests that it’s the same ship. When Kane discovers the eggs, that scene seems very familiar to one in one of the prequels. It could be that the previous mother was hiding in the ship and when she died, one of the babies became the new queen in the later Alien movies.

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    OP was wanting proof-positive one way or the other. Weasel words like "seems", "It could be" and "suggests that" are always warning flags that an answer lacks evidencing
    – Valorum
    May 2 '20 at 9:56

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