We recently participated in a London-based press junket for Prometheus - where Ridley Scott was surprisingly forthcoming about the shared threads between the film and Alien as well as where the director might take the spin-off storyline in the future. Also, keep in mind that our write-up is only one way of interpreting the rich Prometheus mythos and Alien connections - so, if you disagree, respectfully discuss your theories in the comment section below with your fellow moviegoers.
[MAJOR PROMETHEUS SPOILERS BELOW!!!]
Prometheus - Alien Connection Explained
Ultimately, Prometheus does not provide as many direct connections to Alien as some fans might have expected - based on the footage found in the trailers. However, the film lays the groundwork for the subsequent events that would later befall warrant officer Ellen Ripley, as well as the Nostromo crew. Not every "Point A" introduced in Prometheus actually leads directly to a "Point B" in Scott's 1979 Alien film - but there are plenty of ideas and story beats that set the stage - even if they still have to evolve further (off-screen) following the events depicted in Prometheus. As David (Michael Fassbender) points out in the Prometheus trailers: "Big things have small beginnings."
It's a fitting point - especially since Scott had no idea that, back in 1979, his sci-fi horror film would cause so much speculation (not to mention launch one of the most recognizable sci-fi brands in Hollywood):
Ridley Scott: The very simple question was “Who the hell was in that ship? Who is sitting in that seat?” and “Why that cargo?” and “Where was he going?” no one asked the question, so I thought “Duh.” It’s a “duh,” isn’t it? [Everyone Laughs] They’re all bright guys… Jim and David and the French guy, and I thought “Wow, duh.” And I just kind of say and thought about it for a while and I was busy, so I didn’t really do anything about it and then when they finally put it to bed in Alien vs. Predator I thought “You know what? This is a good idea here.”
The more I talked about it, I thought “God damn….” I was going to call it “Alien – Paradise,” because I thought that had a spooky connotation to the idea, because it concocts our notion and idea of paradise and “what is that?” And paradise to us suggests religion and religion says “God” and then God, who created us, and that’s certainly… you’ve got a scientist who believes in God and there’s lots of scientists who believe flatly in God and even though they may be in quantum physics, they say “I get to a wall and some times wonder “who the hell thought of this one?” and I can’t get through the wall. When I get through the wall more is revealed and I still see another wall, so who is making this shit up?”
The question of God and "who created us" is central to the connections between Prometheus and Alien - since the entire plot revolves around a pair of archaeologists, Dr. Elizabeth Shaw (Noomi Rapace) and her partner Dr. Charlie Holloway (Logan Marshall-Green), whose quest to find their creators takes them (along with the Prometheus crew) to the distant moon LV-223. The expedition is funded by a near-death Peter Weyland, founder of the Weyland Corporation, the company that serves as the predecessor to the alien-obsessed Weyland-Yutani megacorp in the original Alien movies. Contrary to prior speculation, LV-223 is not the same moon as the one visited by the Nostromo in Alien (known as LV-426) - since, in addition to different names, the planets feature differentiated atmospheric compositions. As a result, none of the events depicted in the Prometheus trailer (such as an encounter with a "Space Jockey") are directly connected.
While the Space Jockey served as a minor, albeit mysterious, point of speculation for Alien fans, the race takes center stage in Prometheus - and is introduced by Shaw and Holloway as "The Engineers" (since the pair believe the alien race is responsible for the engineering of mankind). However, upon arriving at LV-223 it is quickly revealed that Shaw and Holloway were only partly right - as The Engineers/Space Jockeys didn't just plant humanity on Earth - they're also a genetic match for human beings (meaning they are earlier and more advanced versions of us). Some moviegoers will no doubt remember the Space Jockeys as elephant-like looking creatures but, as has been series canon for over thirty years, Prometheus confirms that the iconic-look of the character is actually representative of the Engineer spacesuits (which feature a lengthy mouth-breathing tube and protective rib-like supports on the chest) - not the life form itself. As a result, the Space Jockey shown in Alien has undergone a fossilized fusing of both body and spacesuit (resulting in the impression it was elephant-like).
Furthermore, during Shaw and Holloway's investigation of the moon, they discover the LV-223 ruins were actually used by The Engineers as a satellite storage facility for an especially dangerous bio-weapon of mass destruction (a weapon they didn't want to have anywhere near their home planet). When removed from its sealed housing (vase-like containers), the slimy black liquid breaks-down DNA in organic matter - outright killing those infected, or in some cases, creating dangerous and horrific mutations (such as a batch of maggot-like worms that mutate into vicious 40-inch long snake-creatures in a matter of hours). While the details of the event are unclear, at some point (which the team pinpoints to be around 2,000 years earlier), The Engineers' facility on LV-223 was overrun by an outbreak of the mutagen - and the local population was wiped out. That is, except for one remaining Engineer who remained safely preserved in a form of cryo-sleep.
Unsurprisingly, a similar fate befalls the Prometheus crew - after Holloway becomes unknowingly infected by the mysterious substance. Inebriated and unaware of his infection, Holloway and Shaw celebrate their discoveries by having sex - which hours later (following Holloway's untimely death), results in an unexpected pregnancy (Shaw is revealed to be incapable of having children). The embryo is quickly determined to be non-human and, while everyone else deals with another infected crew member, Shaw undergoes a gruesome procedure (at the hands of an automated surgery machine) to have the creature cut out of her. Once removed, the fetus is revealed to be a tentacled organism that flails around and attempts to escape before Shaw "sterilizes" the creature until it's no longer moving.
Shaw then inadvertently runs into David, who is tending to a recently unfrozen Peter Weyland - who reveals the true nature of the expedition: with only days left to live the billionaire literally wants to meet his makers (and hopes for some way to avert death from old age). However, when the team heads to The Engineer ship and awakens the survivor, he refuses to play into their desires for answers, quickly dispatching nearly everyone in the party, and resumes his prior mission directive (to pilot the weaponized ship to Earth - in an effort to eradicate The Engineers' human creation). Why The Engineers would choose to create and then destroy humanity is never fully revealed - although it can be intuited, when compared to a line that David delivers - "Who doesn't want to kill their father?" - that The Engineers (despite superior technology) might have been fearful that humanity would one day seek their creators out in an effort to destroy them. Faced with the threat of planetary annihilation, the Prometheus flight crew pilots the ship into the escaping Engineer ship - sending it crashing to the ground - sparing only Shaw and David.
With the threat neutralized, Shaw attempts to pilot the ship's lifeboat but is horrified to discover that her fetus has grown into a person-sized beast. Just as she retreats, the surviving Engineer arrives (in an attempt to finish-off Shaw) and is snatched by the mutated creature's tentacles. As Shaw runs off, the creature forces one of its tentacles down the Engineer's throat and wraps its body around his struggling body - before the alien pair collapse and fall silent. In a pre-credits scene, the lifeless body of The Engineer is shown flailing around - as an adolescent alien queen-like life form erupts from his chest, splitting his body in two. While neither the fetus nor the chestburster/xenomorph creature are fully-formed versions of the species depicted in the original film, given nearly 30 years worth of time between Prometheus (2093) and Alien (roughly 2122) - coupled with the xenomorph's highly adaptable physiology (as well as rapid development) - it's possible that it'd only take a few generations of facehugger-xenomorph queen cycling to streamline both creatures' development into their "modern" forms.
It's a set up that is further clarified when David tells Shaw that they can still escape the planet, since the Engineer's crashed ship is only one of many, meaning that the Queen's progeny could have easily encountered other surviving Engineers who were still preserved inside their ships on the moon - or might have come into contact with Engineers who later visited LV-223 (to investigate the Prometheus event or collect more of the weaponized mutagen). One of these unfortunate travelers could then become the Alien "Space Jockey" - who dies in his pilot chair (and crashes on LV-426) after a xenomorph bursts from his chest (and presumably lays the facehugger eggs that Executive Officer Kane (John Hurt) encounters in Alien.
However, it's also entirely possible that the films are, as hinted at earlier, only loosely connected and the impregnation of Shaw is merely a detour in the mutagen's journey to its final xenomorph form (instead of an entirely unique mutation) - especially considering a massive carving, depicting a xenomorph-like creature, is plastered on the mutagen storage room wall. This would indicate that xenomorphs pre-date the Prometheus event and, regardless of the host, the mutagen carries certain properties which, after infecting a subsequent series of organisms, will produce new hybrid creatures who (over time) evolve closer and closer to their current xenomorph/facehugger forms.
Assuming this theory, it's sill unclear whether The Engineers developed the mutagen or harnessed it from an existing (and ancient) xenomorph population - meaning, in addition to the possibility that more xenomorph-producing mutagen stockpiles could exist elsewhere, there might also be naturally occurring native colonies of the creatures somewhere in space. If this is the case, then it's even easier (albeit less connected) to explain the set up for Alien as well as the death of the original "Space Jockey": the Alien LV-426 event (and 2122 encounter with the xenomorph/facehugger creatures) could have been the product of an entirely separate outbreak of the mutagen - which might have even occurred long before the events of Prometheus (given the fossilization of the Alien "Space Jockey"). Scott even touched on this version of events at the London junket.