Question: What exactly is the space jockey and why haven't we seen it in the other films except its fossilized self sitting in the what I call the laser gun?
Answer: It's another race of space alien that is also subject to infection by the Aliens. This particular one was infected and moved as far as it could from its race's known space and broadcast a warning before it died. The presence of eggs in the hold may indicate that it was a research ship. The race was never used in other Alien movies because it adds a new dynamic to the plotlines: two alien species, locked in mortal combat and neither particularly friendly with humans. In the Alien pseudo-prequel Prometheus we learn these beings are known as the Engineers and have interesting ties with both the aliens and humans as well.
Answer: Other theories, mostly developed in the comics derived from the original franchise, assume the xenomorphs were biological weapons conceived by the Space Jockeys for some interstellar war of theirs. Hence, the crescent-shape derelict was just a bomber, full of eggs and operated by a single pilot to minimize risks of accident with this mostly dangerous cargo. - what just happened though.
AKA, the plot of Prometheus.
Question: How was there a thunderstorm and rain inside the ship while traveling through space?
Answer: That wasn't a "thunderstorm and rain" inside the Nostromo. It was condensation dripping down from the ship's ventilation/cooling system. When searching for the cat, Brett (played by Harry Dean Stanton) removes his cap and stands beneath a cooling shaft, allowing the condensation to splatter like rain on his head and face.
Answer: What scene are you referring to?
Question: How did the company know about the Alien in the first place? Presumably no-one had been there before and the signal they picked up didn't indicate the presence of an Alien lifeform.
Answer: It was never fully explained. "The Company" had a standing directive that any signal detected which indicated alien life was to be investigated and specimens collected and returned. Failure to comply would result in the crew forfeiting their profit shares. The company apparently had previously detected the crashed alien astronaut's warning signal from LV-46 and wanted to search for alien lifeforms without specifically knowing what would be found.
Actually in the movie it is indicated that the company definitely knew about the xenomorphs, given Ash's directive. It is not explained how in this movie but it is in the movies "Prometheus" and "Alien: covenant." The standing directive about investigating signals was just an excuse to use an expendable crew to procure a specimen.
Question: Why did the shuttle craft only have room for two crew members when there are seven of them? The shuttle is mainly an escape vessel if the ship was in danger and their lives were at risk hence the stasis capsules, so there should have been accommodation for seven.
Answer: Considering "The Company" that owned the mining space ship was notoriously cheap (and corrupt) about providing their crew with necessities, it is hardly surprising they had inadequate safety equipment, like enough stasis capsules. Also, the company's real mission (known only to Ash) was to collect the alien creature at any cost while the crew was deemed "expendable," so no need to provide them with a viable escape method.
Answer: It actually appears to orient both ways, presumably Lambert is switching back and forth between orientations. When Dallas turns; it shows on the readout as a 90 degree turn. When Dallas goes down the ladder the first time the readout shows the dot travelling downwards on the screen. It can't do both unless Lambert is switching them. And it makes sense that she would, she knows where he is because he is calling out his location as he goes. Lambert likely knows the path Dallas intends to take and switches orientations when he does. This confusing set-up is purposefully meant to disorient the audience, so they, like Dallas, have no idea from which direction the alien is coming. Lambert seems to have also become disoriented (this seems an impossible task with no line of sight) and can't give Dallas a direction to escape. She has the screen oriented so "forward" is to the right, Dallas goes down towards the alien, so she says "No! Not that way! The other way! God!"
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