Here's a little convoluted notion of mine which I prefer to believe, until Prometheus 2 possibly contradicts it.
- The ghostly images of the Prometheus 'Engineers' that are seen desperately running through the complex due to some 'incident' or other...are showing 'Engineers' who tried to get away from a large (unseen) vaguely-humanoid creature which was created by either a 'goo'-related accident or a 'goo'-related weapons experiment...
...this 'incident' revealed by the 'holo' recording was something that occurred a very, very long time in the past...and it's THAT large creature which then ended up stealing/'piloting' one of the various 'Juggernaut' ships available at the time...
...inside that particular ship were stored many egg-shaped 'bio-weapons' which were originally laid by another type of creature that those long-dead 'Engineers' had some kind of dealings with at the time...and the large creature was attacked and impregnated by a face-hugger from one of those eggs it disturbed when it initially entered the ship...
...however, the creature survived long enough to successfully fly the ship away from LV-223 (where Prometheus is set), but ended up crash-landing on LV-426 (where Alien is set)...due to the chestbuster stage eventually doing it's work...
...and as it crashed, an automatic 'warning system' automatically kicked in from the ship at that point, to indicate that this was effectively now an 'off-limits' area due to the dangerous cargo that had been stored aboard it...
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(On the other hand...if you happen to like the whole 'Engineer' as 'spacejockey' (from Alien) scenario regardless, then instead of a separate, unseen creature, I suppose you could choose to imagine that it was actually one of those long-dead, scared 'Engineers' in the 'holo' recordings who managed to get to a 'Juggernaut' at the time...but then crashed it on LV-426 thanks to being face-hugged)
On the other hand...maybe the 'Engineers' have actually styled their 'snorkel'-like helmets (as well as the one seen on the 'Juggernaut' chair in Prometheus) on something they 'revere'...something that's bigger than them in the scheme of things?...
...something which we saw the long-dead remains of, inside a much older version of the 'Juggernaut' seen in Alien?...
Now, I really must get on with my day.