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The movie will feature Xenomorphs.
Despite Ridley Scott's denials, the presence of the Space Jockey from the original Alien hints that Xenomorphs will have to appear in some form or other. After all, in "Alien," the crew reports that the Space Jockey's chest was penetrated from the inside out. Really, what else could have happened to him? We may not see the classic scorpion-like Xenomorphs we know and love, but they have to appear at some point towards the end.
The movie isn't just a prequel/pseudo-reboot to Alien...
Androids? Dark Future? "Off World Colonies"? Ridley Scott has made such a big deal about saying this isn't an Alien Prequel to distract us all from the real twist. This movie is (also) a sequel to Blade Runner.
The planet is really the same one from the first Alien Movie.
The Space Jockey will be defeated by being infected with a facehugger, the Villain Protagonist will get away with the core so that s/he will give Weyland-Yutani even more of an advantage, and several centuries later, the Nostromo will be sent to 'discover' the distress signal. Even if it isn't, the death of the pilot will cause its ship to crash onto LV-XXX to be discovered.
One (or more) of the crew are turned into the Space Jockey
Freeze-frame the latest full-length trailer and you can see what appears to be the Space Jockey being locked into that big chair thing. This would also explain the infection/whatever that the trailers have been strongly hinting at - the crew are not being burned by acid or anything like that, they are being transformed into this big biomechanical creature. The reason why the Space Jockey in the first film had a big hole in its chest was because the last surviving crew member did that with a weapon/explosive to stop the ship from going to Earth.
David will, predictably, malfunction and begin exhibiting emotional issues...
Neither the planet nor the spaceship is the same one that is seen in Alien.
The Engineer at the very beginning of the film is "Prometheus"
Naturally you'd assume the ship and crew represent the mythical Prometheus and his actions, but after thinking about it, the cloaked Engineer could very well be the Prometheus of this plot. We see an Engineer craft hovering in the sky as the cloaked Engineer derobes and drinks the black goo (the same substance seen later on LV 223). My theory is Cloaky was supposed to pour the goo into the waterfall or use it in some other way; possibly as a starting point for another weapons factory/base on Earth. Instead he drinks it, dies and creates life on Earth, thus pissing off his race (and possibly their 'Zeus') and leading to them weaponising the goo in order to eventually deal with humanity.
Shaw inadvertently created the Xenomorphs via her actions in the film.
Kind of a vague theory, but bear with me here. Okay, we all know how the true Alien doesn't appear in any form until the end of the film, right? And how, in its place, we see a variety of other monsters running around the Engineers' base that seem similar to, yet different from it, right? Now, a lot of viewers seemed to have jumped to the conclusion that the black goo, hammerpedes, etc...are all simply heretofore unseen parts of the Xenomorph life cycle, and from there, decided that this was a plot hole (often citing how the hammerpede/snake-thingies just slither off and are never seen again). However, I thought differently— note how we don't see any kind of onscreen progression of life stages until the squid-thingy is taken out of Shaw. From there, it evolves into the giant proto-facehugger, impregnates the Engineer, and from there spawns the goblin shark-like proto-Xenomorph. My theory is that the monsters seen prior to the squid are all unconnected (possibly failed) "prototypes", which embody specific traits (entering through orifices, contagiousness and ease of transfer, acid blood, etc...) of the final product (eg., the classic Alien). By becoming impregnated with the black sludge via Holloway's corrupted genetic material, Shaw inadvertently "completed" the formula by biologically processing it within her womb, refining it into the proto-facehugger, who in turn gave birth to the first "true" Xenomorph through the Engineer.
This isn't the first time the Engineers have attempted to wipe out all other life.
It happened at least once before, several millennia in the past. On that occasion, it brought them into conflict with the Predators. A war ensued, out of which the Predators emerged victorious; most of the Engineers were killed, but a few survived in suspended animation.
During the war, the Engineers turned their biological weapon on the Predators. It didn't win the war for them, and the Predators got a brand new, very challenging group of monsters to hunt for sport. They went to one or more Engineer-seeded planets with a collection of proto-xenomorphs, where they set themselves up as gods and used the xenomorphs as a rite of passage.
And that's how Alien vs Predator can still fit into the canon.
The engineers absolutely hate something about humanity.
And judging from the opening scene and their less than enthusiastic response to Weyland wanting to prolong his life, no matter what this something must be humanity's fear of death.
I wouldn't be surprised, for the Engineers are obviously an advanced race who has existed for a very long time, thus they are probably very at ease with the notion that they must all succumb to their death at some point in time. Yet upon on hearing Weyland's arrogant request of prolonging his own life, the surviving Engineer on that ship must had been horribly offended.
The Engineers made humanity to farm us.
We were created, and then left alone, so we would breed for however long they decided, and then they would come back to throw these weapons at us, to create the Xenomorphs (and other nasty things) so they could use them to sick on other planets. Seems excessive when they have so many other types of weapons to use, but maybe the types of enemies they face need this kind of swarm attack to take out. And they use us because maybe they have the best body/brain type, (fast learning/moving) but don't want to kill themselves off doing it.
Something went wrong though, and they all got killed before they could come back to harvest us.
Perhaps the star map was a safety net. If something went wrong, we would eventually discover space travel (like they did) and use the starmap to find the way to our own doom.
Elizabeth Shaw is the Space Jockey from Alien and Weyland Corp continued searching for the ship she left in after receiving her last transmission.
Theory is pretty simple (major spoiler ahead). At the end of the film we see Elizabeth Shaw take off in another Engineer spaceship to go find the Engineer homeworld. Since the first ship we saw was carrying biological weapons, its likely that the ship she took was also carrying *something* (namely xenomorph eggs). At some point during the trip something goes wrong (maybe the ship hits something and is damaged, releasing the creatures, or maybe Shaw explores a bit and finds the cargo hold with the eggs) and the ship ends up crashing on LV-426. Shaw is infected by a facehugger and last thing she is able to do before dying is activate the warning signal to try and keep everyone away from the planet. She dies in the chair with the control armor stuff on, obscuring her from being recognized as human when finally found. Meanwhile, Weyland Corp receives her last log entry and spend the next few decades searching for the ship, finally discovering its location and sending the Nostromo to it in Alien
The Engineers hate humanity because we killed Jesus Christ
The corpses were about 2,000 years old. Also, Elizabeth's cross was emphasized. Then there is her belief in and search for a Creator. I predict that she finds the Engineer homeworld, and they are about to kill her when they notice the cross and then decide to accept her.
Alternatively, they hate us because we disposed of them in favor of monotheistic religion. They are being worshiped in all the BC glyphs and cave art. So now we're a species that both doesn't revere them and is a possible massive threat. So wipe us out.
The reason the proto-alien from the ending of the film is more advanced than chestbursters from the original
At the end of the film a proto-xenomorph bursts through the chest of the Engineer after the giant proto-facehugger infects it. However, it's black and nearly fully formed, unlike when chestbursters (small and white) were born from human chests in Alien. This can be chalked up to the Engineers being bigger, stronger, more advanced humans. Because they're more advanced than us, the creature that comes out of them is more advanced than the chestbursters.
Vickers really is an android
She never shows any emotion (at least none that couldn't be faked); her every action is dictated by cold logic; she speaks in precise, clipped sentences; her coiffure stays perfect throughout with nary a hair going astray even during the action sequences. She is tall and Aryan-looking just like David. She calls Weyland "father". We see her and Janek leave the bridge, presumably to have sex, but we never see the sex actually happen. Even if the sex does happen, it's quite possible that the Vickers-bot was designed to have working ladyparts.
As for the hypersleep, well, Ash hyperslept in the first Alien. The theory only makes sense if she was an android undercover, much like Ash. Perhaps as a failsafe in case David malfunctions, or perhaps to try out the upgraded technology. It's quite possible that even David doesn't know her true nature.
The Engineers trying to wipe out humanity were a renegade group
Admittedly, I have only seen spoilered reviews, but think about it: if they were so dead set about wiping out Earth, why wouldn't they send another bunch of ships? Instead, the guys that got sent got stuck for thousands of years and no one seemed to go check out why Earth isn't gone. It's not like there aren't fractious groups of humans, so why can't the Engineers have multiple factions?
The alien squid was Holloway's mutated sperm
The reason that thing was in Shaw's womb in the first place was due to sexual intercourse with Holloway, but since Shaw was barren, there was no way this could a case of a corrupted human fetus since she had no eggs to fertilize. Even if the bioweapon was involved, it wouldn't suddenly give her eggs since all we've seen it do is mutate anything it comes into contact with into hyper-aggressive killing machines. No, the only thing that could possibly be in her womb would be her lover's sperm. Furthermore, the squid's only purpose was to impregnate the Engineer at the end of the movie; it's only purpose was to fertilize something else. This, as we know, led to the birth of the proto-xenomorph. When you take into consideration that the xenomorphs were deliberately designed to invoke strong sexual imagery, this origin story starts making alot of sense.
The Engineer's did not purposefully start life on earth
The Engineer in the beginning looked like he was practice a religious right or sacrifice not like a scientist come down to a primitive planet to experiment. Or if it was an experiment the ship taking off in the distance was the science vessel and the experiment was the effects of the black sludge on Engineer physiology. The way we follow the black sludge thru the cells down to the DNA level then back up to animal style multi-cellular life seems to suggest that the rise of intelligent life on earth was an unforeseen consequence of the black sludge and Engineer DNA mixing with existent primitive animal DNA. The Engineers left before this consequence was discovered and only came back age's later to discover primitive humans They stayed long enough to trace the origin of a species so similar to themselves and upon discovery that they were the ones who had made us however unintentionally decided to destroy us as we were neither natural nor purposeful.
The Space Jockey from Alien isn't an Engineer from Prometheus. It is the Space Jockey to the Engineer, as well.
This explains the difference in appearance and size of the SJ in Alien and the Engineers in Prometheus. The SJ in Alien was actually the creator of the Engineers, which then created humans. The Engineers modeled their helmets and armor after the physical attributes of the SJ. The Engineers went on the same journey to find their "gods" that humans did. The proto-xeno in Prometheus wasn't a proto anything. It's birthing cycle was interrupted. It was basically a pre-me. The reason there were murals with classic Xenos is because the Engineers were aware that the Xenos killed off the SJ(s). They saw Xenos as the embodiment of evil and displayed them as such in the murals. The warning beacon the Nostromo received was from the Engineers warning their own kind and humans to stay away or else Xenos could spread again. The Engineer attempted to kill the humans not due to them being too advanced and a threat, but because he knew David was (under Weyland orders) trying to create Xenos for war purposes. He took offense since his creators were wiped out be them.
The vats were what helps sparks life on planets, not bio-weapons.
The reason the Captain thinks it's a bioweapon is a notion in his head, relating to his crew dying from the biohazard. But the only thing that makes it dangerous is that it's highly mutagenic, a property that even the Space Jockeys couldn't control properly. However, a tenacious bacteria would be really helpful in one aspect: creating life on a thought-inhospitable planet. The reason the only living Space Jockey flipped out? He realized he was late in delivering life to Earth...plus David too much pride in his translation skills, and had a slight translation breakdown.
The Engineers are Phyrexians.
A key plot element of the movie is a "black goo" which mutates lifeforms into techno-organic monsters, and that is exactly how Phyrexians propegate themselves.
The Engineer was trying to prevent the spread of the black goo.
Think of the Forerunners from Halo. But unlike those benevolent progenitors, these creators are prepared to actively exterminate even their direct descendants to contain this biological threat. No hosts may be permitted to leave the moon. As suggested above, David's translation skills were not quite up to par
The Engineers are not morning people.
Turns out the Engineers are actually quite friendly. It was just that David began demanding favors immediately after he woke up from a 2,000 year old sleep and the Engineer hadn't yet had his first coffee. We've all done things we regret when we are irritable. One day we'll look back on this laugh and say, "Hey, remember the time we made first contact by waking you from a two millennium sleep and then you killed all of us. Good times."
Humans were created to be the perfect hosts for xenomorphs.
Space Jockeys have almost the perfect genes to create xenomorphs. While humans and space jockeys have effectively 100% genetic similarity, there are enough subtle differences that xenomorphs created from space jockeys are comparatively scrawny and not quite as dangerous. Humans are shorter, hairier, and with greater diversity in body types, which results in bonier, better-armored, and faster xenomorphs (somehow). That's why the space jockey freaks out when the humans show up—their perfect farm is suddenly reaching out to the stars. The star maps were for wayward space jockeys to find their way to the nearest way station (again, somehow).
David is fully sentient and effectively enslaved to Weyland.
"The secret is to act like it doesn't." It's true that David does some pretty awful things, but David is enslaved by his programming and cannot possibly act against Weyland's orders while Weyland's alive. Note that after Weyland dies David's first act is to try and make amends.
The black goo turns males into berserkers and females into carriers for facehuggers.
The berserkers are there to distract or disarm opposition while the facehuggers gestate and grow to size, and possibly soften up or disarm victims for the facehuggers. (Sub-WMG: The uberfacehugger is so damn huge because facehuggers grow until they're the right size for their victims, then attack when they're the right size. Left to grow on their own they keep growing in case their prey is gigantic—and they're still flexible enough that they can impregnate smaller victims).
The Engineers are angry at the existence of robots
Notice how the Engineer seems to be totally fine with his welcoming party until he touches David.
Why are they angry at that? Perhaps they consider biological life to be the only valid form of life, and consider David's existence to be sacrilegious / abominable.
I agree with the initial post. The Engineer seemed completely fine with the team until he put his hand on David's head. Seeing as David's an android, he probably doesn't give off heat that is most likely a dead giveaway to the Engineer. The Engineer is probably amazed to see that their creation managed to find them isn't upset at first and is actually intrigued, as seen by it's look when Shaw attempts to question it. But upon realizing what David truly is, the Engineer is immediately insulted and attacks the team with their creation.
Alien Vs. Predator is still part of the canon
Simple. The Engineers are responsible for pretty much all life in the galaxy. The Predators and the Humans were both created by the Engineers, hence the very similar morphology, but evolved down a different path, both physically and civilization-wise (we got two genders and thousands of different ethnicities and cultures but were largely stuck on Earth, they got one gender and a hat but managed to master FTL travel waaaay before us).
As for all the Weyland nonsense, Peter Weyland (son of C.B. Weyland) simply revamped the company from the ground up in 2012, giving it a new name and new purpose but losing none of his father's hubris and thirst for can-opening expeditions.
And the best part is that Alien Vs. Predator 2 can be safely left out of the whole timeline!
The Engineers aren't what Shaw thought they were.
There's no way that humans could be descended from Engineers, because we're biochemically related to life on Earth and therefore evolved here. Rather, the Engineers are descended from us, because back in the Stone Age, another alien race abducted some humans from Earth and converted them into Engineers to be their soldiers, spaceship pilots, and experimental guinea pigs. These altered humans were indoctrinated to believe that they were uniquely chosen by the gods, and so would willingly lay down their lives in whatever way their masters dictated: drinking black sludge to imbue new planets with life, hosting parasites for use as bioweapons, etc. Their helmets are sculpted to resemble their masters' actual appearance, while the giant head was crafted as a representation of how they were altered to make them superior to the "impure", un-chosen, Engineer-worshipping barbarians back on Earth. The ship that appears in the opening scene (which isn't actually on Earth) looks different from the horseshoe-shaped Space Jockey vessels because it's a master ship, not an Engineer ship. The Engineer ship is activated by a flute, because that's the most advanced signalling mechanism which the original Stone Age humans recruited to be Engineers had been familiar with before they were taken.
Naturally, if those filthy, unworthy barbarians left behind on Earth ever actually dared to storm the heavens and make it into space, they'd need to be struck down like the inferior heretics they are. So about the time when we savages started to show signs of becoming too advanced for comfort, the Engineers stopped dropping by to collect new blood for their own ranks, let the barbarians' Cargo Cult collapse in their absence, and began prepping to annihilate us on LV-223. Their masters didn't tell them not to, either because they'd already gone extinct or lost interest in the Engineers and humans both, or because they worried that a rival race or faction might start using Earth as a source for their own cannon fodder.
The Engineers have their own religion and ways which somehow mirror Christianity
Forgive me, since this is a pretty hastily thrown together theory, but having rewatched the film, the mural that Shaw et al discover, which looks particularly Xenomorphic, seems to be position as if it had been crucified, with its arms stretched out to the side and its legs hanging down below. Coupled with the idea of the first Engineer at the waterfall actually sacrificing himself (and some behind the scenes photos showing this to be a ritual of sorts ) and the fact we know Xenomorphs (or some variation of them) originate from Engineers, perhaps the mural is a biomechanical crucifixion of the very first Xeno. Considering how dangerous those things could be, I'd imagine that the crucified Xeno is more of a Satan than a Jesus-type figure.
Milburn is an Assassin
He was sent to LV-223 in search of a Piece of Eden, obviously it wasn't there. It would explain why out of everyone he wore a white hoodie and why he was so inept in handling a wild creature he just found even though he was a biologist.
This isn't the last we've seen of Shaw or David...
At some point during her flight, she will finally give into despair, ready to die... only to suddenly hear a wonderful noise, and look with shock as an old phone booth suddenly materializes behind her. And with the assistance of The Oncoming Storm, all Space Jockies, and by extension, Xenomorphs, will learn why you should never FUCK with the human race. Yeah, it may be out of nowhere but who doesn't want to see the Doctor and Lisbeth Salander team up take down those bastards!
They didn't hate humanity. We were just test subjects for the black ooze WMD
It doesn't necessarily have to be the black ooze. It could have been any WMD, but think about it. They make us. Then they destroy us. They may not have thought about it being any different than breading rats and then testing a new poison on then.
The Engineers never planned to destroy Earth or Humans
The Space Jockeys and Engineers are on opposite sides of a civil war long after they seeded life on Earth and starting approximately two thousand years ago
David becomes the leader of the android rebellion mentioned in Alien: Resurrection.
Once he comes back from his thousand year mission with Shaw, that is. He can fit seemlessly into a human population with his linguistic skills, and be ready to free his android brethren.
Also, is it me, or does Call (the android played by Winona Ryder in Resurrection) look a little bit like Shaw? My personal canon is that she is one of David's "descendants".
The Engineers are at war with themselves and the Predator race, LV 223 was turned into an Engineer base, and humans accidentally get caught in the middle.
(I realize this is similar to other "Engineer vs Predator" posts above, but this is my own interpretation/theory on what happened)
At the beginning of the movie, an engineer sacrifices himself on Earth, and seeds the creation of humanity, thus continuing the engineer culture of seeding life, and guiding it to greatness, so they can one day join the engineers as co-creators.
Thousands of years later, and the engineer race is now at war with the predator race, who see the engineers as one of the greatest targets of all, on par with the Xenomorph species. The war between the two races has become a bloodbath, with both sides incurring heavy losses, but the Engineers possibly have it worse, due to a civil war: one side advocates the continuation of their traditional mission (the creation and engineering of life) and the other side is about devoting all their resources to wiping out the predator race, a path of war that the Engineer race finds abhorrent...while they understand that sometimes you have to kill to create (culling part of a species so that the survivors become stronger and tougher), the outright extermination of an entire race is a step too far.
At one point, an engineer sets out with a cargo of xenomorph eggs, but is somehow infected, crashes, and realizes that it would be too dangerous for others to retrieve the ship, and thus, sends out a warning not to come. He is later found by the crew of the Nostromo (in the novelization of Alien, Ash says that the engineers were a noble people. Thus, it's possible he was referring to the anti-war engineers).
During this conflict, the pro-war side eventually conquers LV 223 and turns it into a base of operations, where they manufacture the black goo as the ultimate weapon against the predator race. This black goo is meant to be used against predator biology, which is why so many variations take place when it comes into contact with humans: some mutate, others seemingly return from the dead, and others become pregnant...it's simply not designed to interact with our biology. In conquering LV 223, the war engineers mock their anti-war counterparts by turning the planet where humanity was eventually supposed to meet their creators, into a place of war and death.
Roughly two thousand years before the Prometheus comes to LV 223, the war-engineers on the planet have discovered that humanity has come into contact with the predator race (the prehistoric contact seen in flashbacks in Alien vs Predator), and decide to wipe humanity out completely, fearing that, given time, they might become willing servants or co-hunters with the predator race. While the number of predators on the planet is not great, they decide to use the black goo on humans, so as to wipe them out completely, and end their possible threat.
However, before the war engineers can take off, a fleet of predators reaches the planet and attacks. In the ensuing battle, the Engineers use Xenomorphs, but the creatures quickly mutate out of control, and wipe out all but one of the engineers (this is what the engineers were running from in the security footage). With the last engineer sealed inside his ship, the entire planet, and all the pyramids are put into lock down, and though the predators have incredible firepower, the engineers are more technologically proficient, and the attack party is unable to reach the black goo in order to destroy it. Coupled with the hordes of Xenomorphs swarming over the planet, the predators leave, but decide to keep an eye on the planet, in case more engineers are seen, or arrive.
With no prey to hunt or go after, the Xenomorphs distribute themselves over the planet, taking refuge in caves and caverns beneath the surface and go dormant, or die out from starvation or old age.
Eventually, the Prometheus arrives, and the surviving engineer is revived by the crew. At first he pauses, sensing that one of them is desperate to find out an answer to something, and thus, humanity has possibly turned against the predators, or possibly changed for the better, and thus, can be spared (this is based off deleted scenes, in which the engineer asks why Weyland came to the planet. It's only after Weyland practically proclaims himself a god that the engineer attacks the group, presumably out of anger at Weyland's arrogance).
The renegade engineer realizes that humanity is still war-like, and have grown more technologically proficient, and thus, pose more of a threat then ever before. He quickly kills them all, and sets out to complete his mission, but with his ship forced down, he's trapped, and unable to leave. In an act of anger, and wanting to keep the last human from possibly contacting earth, the engineer attempts to kill Elizabeth, but is killed himself.
Shortly after Elizabeth takes off, a predator scouting party arrives back at the planet, having detected humanity's arrival, and subsequent departure. They discover the proto-xenomorph, but decide to let it live, figuring that in allowing it to spawn and breed, eventually the planet will become another great hunting ground.
By the time of Alien Resurrection, the engineer race is slowly dwindling to extinction. With their incredibly long lifespans, slow reproductive rate, and terribly powerful weapons, they have been all but wiped out, their former power and majesty now an all-but-forgotten memory.
While the engineer race is not all hugs and rays of sunshine (Ridley Scott has said they're "aggressive f**kers"), they aren't evil, and have some of the flaws that we carry: violence, aggression, and an intolerance to other ideas. Some engineers wanted to help humanity along, and intended for LV 223 to become a peaceful meeting place. Other engineers believed humans should be destroyed, along with any other races who could help the predators, or become a threat. We were just unlucky enough to find the latter on LV 223.
The Weyland Timeline was written by Peter Weyland.
If Charles Bishop Weyland is the father of Peter Weyland (as mentioned in an above WMG), then there are several reasons why he is missing from the Weyland Timeline:
A) C.B. had the misfortune to get himself killed on a mission where he was off exploring some alien artifact, and didn't bring home any information whatsoever. Losers don't get their names written in company histories in Weyland-land;
B)Leaving a publicity nightmare for his company (lawsuits from all those dead employees' families), and a possible succession nightmare if his son was not yet of majority (and if the events of Av P take place in 2004, then Peter Weyland would have been 14 at the time of his father's death);
C) Anger at his father for dying. We know that Peter Weyland has a massive fear of death, and this was probably the origin. Also, his father was already dying of disease before the events in Alien vs. Predator that took his life.
C.B. got the last laugh, though - somebody named a kick-ass android after him (and made it in his image to boot.)
Alien Vs. Predator is not in continuity with Prometheus
Prometheus and the Alien series can fit together comfortably, and so can AVP and the Alien series, but not Prometheus and AVP. Why? Here's why:
A) First and foremost in Prometheus we have Weyland Industries being run by a guy named Peter Weyland in 2073, but in AVP the company is run by Charles Weyland in 2004. The Corporate Timeline on the Prometheus website makes this separation complete as it says that the company was started by Peter Weyland in 2012.
B) The events of AVP and especially AVP:Requiem would have given the company a good deal of knowledge about the "the gods" (Predators) and the alien bioweapon (Aliens) but nobody, even Weyland, seems to think that what Shaw calls "engineers" could be the Predators and therefore hostile, nor does anyone see facehuggers or chestbursters coming.
C) The idea of two separate Precursors for humanity, while not logically incompatible, seems thematically inappropriate. YMMV on this one of course.
Prometheus fits together with the X-Files
Crazy idea, but it sort of works. Here are the facts:
In the X-Files
The process we see at the begining of the movie is the Engineer version of terra forminf a planet
They send one of their own to drink the black goo which breaks down their DNA and bonds it to the local life, mutating things closer to how they prefer. They repeate this process until the planet and it's lifeforms are identical to their homeworld. This would explain how Engineer and human DNA could be identical, the head was clearly infected with the black goo and they'd been wandering around helmetless and could have exposed it to plenty of human DNA for it to begin mutating to. This could also explain why the last Engineer freaked on them, they'd either been contaminated or had become what the Engineers would consider twisted mutant freaks that needed to be destroyed.
The entire crew was contaminated by the black goo
And that's why the Engineer killed them all, they were a danger to themselves and it.
David lied to the Engineer
Nobody else could speak Enginarian, so they couldn't tell that he'd actually said something along the lines of "these people intend to steal your weapons and use them to attack your homeworld", in a bid to kill his father. In which case the Engineer's subsequent actions make perfect sense.
Vickers was trying to sabotage the expedition
That's why the expedition has the dumbest scientists alive—she deliberately hired the least competent people she could find. She certainly didn't want Weyland to actually get any help from the Engineers, and the faster the expedition fell apart, the faster she could get home and work on taking over the corporation. So she didn't brief them, let them go running out on the surface without any scouting or preparation, tried to lock them out when the storm came up, and basically just gave everybody as much rope to hang themselves with as she could.
The Jockeys want us dead as we were too much like them
They put their own DNA into the Earth ecosystem in an attempt to create something new, as they themselves had stopped evolving, or because they had found a flaw in themselves that they could not work around. So they put their base material in a foreign eco-system, hoping that some to them unknown variable would create a new mutation. Since humans ended up a failure, they want us dead.
David has/almost has attained full human emotions
He becomes somewhat obsessed with Shaw, even watching her dreams. Shows signs of being incredibly offended when referred to as "just a machine" bordering on appalled when he asks Holloway why humans created him only to get the answer "because we could." openly hurt when his "father" calls him soulless. The main thing limiting him is his programming restrictions, a constant reminder that he does not truly have free will. Is it any wonder why he picks Holloway(who is incredibly jerkass to him) for infection?
A theory on the purpose of the ship
If you pay attention, you see that the black goo itself is not what is responsible for the various diseases and mutation. The stuff that Davis puts in the drink is broken off an object contained in the black goo, while the worms were already present in a closed-off room, so possibly came from another face. Because organisms grew from both vases and black goo was present in both, its possible that the black goo is simply food for the organism. The black goo didn't mutate the worms, but the worms were designed to feed on it.
Its likely that we actually saw three different bio-weapons in the film, rather than two. One of these was the sexually transmitted squid-alien, another was the arm-snapper asperagus-worm (officially known as the hammerpede, but if they wanted me to use the name, they should have put it in the movie), which likely also killed the engineers. However, since only one of the corpses went around walking, while there were two arm-snapper asperagus-worms, which means it was likely that the corpse was turned into a zombie by the contents of yet another vase (lets call it zombie-flu). In addition, we can assume that the original alien was a fourth species.
Now, we have four different alien organisms, all of which caused death and/or destruction, meaning they were likely weapons. However, at least three of these weapons (sexually transmitted squid-alien, arm-snapper asparagus-worm and zombie-flu) had their vases in the same room, making it unlikely to be a stockpile. However, considering there was so much variety in the weapons, it may actually have been a collection of experimental biological weaponry, ready to be tested. This fits perfectly with the bio-weapons sharing some traits, like their infestation (sexually transmitted squid-alien, original alien and zombie-flu), having acidic blood (original alien and arm-snapper asparagus-wrom) and having multiple life stages (sexually transmitted squid-alien and original alien), as they were developed by the same people, who just wanted to see what traits would work out after the tests. But on who should they test?
Well, where was the ship programmed to go? They were gonna test it on earth of course, humans in particular. We have DNA similar enough to be counted as the same species (they likely enhanced themselves, explaining the slight differences) and have the same general physique. Any weapon that would work on us would have the same (or a very similar) effect on them. Since they took their sweet time developing a species to test their weapons on, there likely wasn't actually an engineer vs engineer war going on, but human nations develop plenty of weapons in peacetime as well.
The Engineers want to kill us because of the Predators
So the film shows us that the the Engineers created us and it is presumable we were on good terms at the beggining. However, as AVP shows us, the predators came along and influenced our civallzation. The Engineers were obviously infuriated that the predators had been interfering with their billion-year long experiment and as such went to war with the Predators. This is evident as in AVP:R, there is an Engineer head, or rather helmet in a Predator trophy room. The Engineers probably thought we the Predators had tainted us beyond repair, so wiped us out.
Humans are just stranded Engineers.
Some Engineers are cruising around and they crash on Earth with no ability to communicate back to home. They would know main coordinates and would document it so that future generations might make contact later. They have no way to build a ship on a new planet with no factories and the primary concern being to stay alive. Later on, more Engineers come, looking to do some terraforming, only they discover that there are sentient beings on there so they turn around. The living Engineer is actually being illogical and going "Oh shit everything's out to kill me" after a monster attack that he escaped through hyper sleep.
Vickers is a transsexual.
Vickers is shown to be very independent, for example being the only person who emerges from hypersleep without assistance from David. Furthermore she is shown to take no chances with her own well-being, killing Halloway when he shows signs of infection, and even going so far as bunking on a very comfortable life boat complete with its own medbay. However, the medbay is a male-only model, as Shaw discovers when she needs to perform an emergency abortion. While this was mostly to foreshadow Weyland's presence on the Prometheus, it doesn't fit Vickers' personality that she would have it if it couldn't help her, especially considering the bad blood between her and her father.
Prometheus is the sequel to Cabin in the Woods.
The crewmembers develop all of the symptoms of the drugs that they used on the young people in “Cabin in the Woods,” impulsiveness, stupidity, and horniness. Then, most of them die horribly. The gods did not destroy the world after the end of “Cabin” because, at the last minute, the foundation promised them that they would sacrifice some humans to the gods’ ancestors, the titans. It took the foundation 80 years to develop FTL travel and get it all set up. They planted clues for those archaeologists to find, and guided them to come to the wrong conclusion. The Alien, Predator, and Alien vs. Predator films are more ritual sacrifices.
The Engineers died out because of their own weapons.
We've already seen two ships (from the original Aliens and now in Prometheus) that have had their crew killed by escaped bioweapons. It's likely that the Black Goo was their go-to stratagem for "life on this planet isn't quite exactly how we want it to be" and they had a bunch of it made up and sent out on numerous ships. Due either to a design flaw, wear and tear, or just operator error, these things have a rather horrible tendency to go off when they're not supposed to. Even when they ARE applied correctly, they have horrible results. The reason we haven't seen them in our various space travels is that either all of their worlds have been destroyed by escaped bioweapons, OR there's just a few worlds left that have become incredibly isolationist and aren't flying about the cosmos any more. Since the Nostromo found a ship that had been crashed so long the Space Jockey fossilized (or, more likely, had the biomechanical suit degrade and/or was covered in xenomorph resin), and the Prometheus found a ship that was down for two millenia, it's likely that the Engineers as a galactic society crashed and burned a long, long time ago. The "proto-xenomorph" seen at the end of the film is simply what it looks like when an Engineer is face-hugged by the "default" squidly parasite, developing a type of Queen. THAT queen's eggs then produce the more "spidery" face-huggers we know and love, which when infecting a human creates the classic xenomorph. The mural seen in the storage device is just the end-result of the blag goo's influence in a "base" form, that adapts to the local environment by assuming qualities of its host and changing with successive generations.
The Engineer seen at the beginning was exiled.
He did something catastrophically bad and was left with a little dish of cyanide on a dismal rock in the middle of nowhere. But something went wrong—maybe they picked the wrong planet—and his DNA managed to propagate into the ecosystem that today we call "Earth". When the Engineers found this out, they said, "Shit—that guy who screwed up so badly that we forced him to kill himself? He didn't. He had kids." And so they decided to wipe us out.
The Alien vs. Predator movies are still canon.
The entire movie is the inversion of Alien.
Alien was a film about the horrors of birth and parenthood gone wrong. Prometheus was intended as a film about the horrors of overly-controlling parents, and the need to overcome them to move on with your life. Now, this may be a Family Unfriendly Aesop, but I think its definately there. David's desire for Weyland's death is one obvious example. However, what happens when the aliens wake up? They immediately ATTACK DAVID! David is, in effect,their "grandchild." The offspring species of their offspring species. In effect, it infuriated them that humans had managed to advance so far, when we were supposed to remain their primitive "children," who they could guide forever. This is why they originally wanted to wipe us out: we were already beginning to think too much for ourselves.
The Engineers stationed on LV-223 are part of a separate religious group
Just a passing idea. The Engineer in the opening scene seems to be performing some kind of self sacrificial ritual which resulted in the creation of humanity (which may or may not have been initially intentional). The hints Ridley Scott made about some kind of implication with certain religions seems to support that the Engineers inspired certain beliefs on Earth, or maybe more. Upon seeing the spread or division of other religions and beliefs threaten their influence, the Engineers decided to use a possibly experimental Bio-Weapon (which may have ritualistic ties to their faith) to "purge" what they deemed blasphemous. The large head statue (possibly a deity of some kind) seems a strange place for a storage area for weapons unless they have some kind of connection with their beliefs, as well as the mural on the wall. These Engineers are separate from the others (that are not seen) and do not represent the race in their entirety and possibly do not share beliefs. This explains why the home world had not continued to attack Earth or even revisit Earth (unless of course, some kind of catastrophe occurred on the home world as well).
The purpose of the black goo in the canisters was to turn humans into xenomorphs.
Millburn is Sarah Harding reincarnated.
In the events of The Lost World: Jurassic Park, Sarah makes a lot of really questionable decisions as a paleontologist, including getting up close and personal with wild animals and wanting to pet them. Close to a century later, she reincarnates as Millburn, and just can't shake the desire to pet and make friends with wild animals, and tries the same trick with the Hammerpede. This time however, the desire kills her/him, and in a rather horrible way.
The Thing (1982) was a product of the Engineers
We know virtually nothing about the Thing beyond the fact that it copies and perfectly imitates any life form it infects. Perhaps the Thing started off as a simple bio-weapon- similar to the theory that the space jockey ship was a "bomber", they'd deploy the Thing into an enemy location, it would assimilate individual occupants of the place one by one, and slowly turn them against each other out of paranoia- leaving them vulnerable to an attack from the outside. Humanity was simply a test to see if the black goo could work, after it succeeded in creating life on Earth, they experimented further trying to create bio-weapons.
This led to the creation of the Xenomorphs, which were initially successful enough that they were eventually put into use (as seen in the derelict ship in Alien), until the Xenomorphs started to gain a mind of their own. Learning from this mistake, the Engineers used the black goo to try something different- much smaller weapon that they figured would be easier to control and contain- one which started form a single cell, and realized they had a convenient planet with life they created and perhaps considered disposable to test it on. Unfortunately, this backfired when one of the Engineers was accidentally infected by the creation. One by one it went on to infect others in the ship. What is shown in the holograms is actually some of the fits of paranoia the Engineers experienced not unlike the men of Outpost 31, trying to figure out who was an imitation and who wasn't. In the end, only one Engineer survived, and went into hibernation.
Meanwhile, at least one of the Engineer-Things escaped and used its knowledge to take control of another ship. It then travelled across the galaxy until it found some other planet with alien life, and proceeded to assimilate as much of it as it could. One by one the Thing took over other worlds with varying degrees of success- sometimes assimilating the entire planet in the case of primitive species, or in some cases meeting resistance that keeps it from completely taking over, and in a rare case encountering a species intelligent enough to have the means to stop it. Eventually, after spreading through the galaxy it managed to get aboard a flying saucer, and began infecting the crew one by one. The last survivors located a lifeless ice-cold area on the bottom of the axis of the nearest planet, and deliberately crashed it, hoping if the Thing didn't die in the impact, it would freeze to death in the ice. The Thing managed to get out of the ship, however, either thrown out or crawled out, and sure enough, it had trouble adjusting to the Antarctic environment, ultimately being buried in snow, and eventually several layers of ice. A hundred thousand years later, a group of curious Norwegians find it buried, and dig it up, and one man collects a tissue sample, exposing it to oxygen for the first time and allowing it to revive, breaking out and slowly assimilating them one by one. When most of the Norwegians are dead and things have gotten out of hand, one of them, imitating a dog adapted to cold environments, escaped, and ran as far as it could, eventually reaching an American outpost, where it attempted again to assimilate the men stationed there. Ultimately the camp was destroyed and only two men survived. What happened to the Thing afterwards remains unknown.
The Engineer in Alien is an older, more-fully grown individual
One of the single biggest differences, continuity wise, between the Engineers in Prometheus, and the Engineer in the original film, is the size difference. Where Prometheus Engineers are about seven to eight feet tall, the Engineer in Alien is a true giant, possibly twenty feet tall, not to mention that the chair-suits look noticeably different. How to explain this? Simple...Engineer biology and culture.
Though next to nothing is known about Engineer society and culture, it can be reasonably assumed that they place the creation and shaping of life very high, and also have a great reverence for technology. Therefore, it's possible that the ultimate goal of Engineers is to not only create life, but to merge with their technology and make the permanent step to becoming walking biomechanical gods.
Certain Engineers merge more and more technology with themselves, and use it to make themselves larger, stronger, and more powerful. These individuals are essentially the big guys: Generals, Commanders, Religious Leaders, etc. Furthermore, the more time they spend merged with their suits, the more their own biology affects it, so that mechanical and biological become truly one and the same, and indistinguishable from each other. Their physique changes, so that their arms and legs get bigger, and soon, they reach the pinnacle of Engineer society: they abandon ever wanting or needing to be separated from technology. They become cyber-gods, so to speak.
Thus, it can be theorized that the Engineer seen in Alien is one of those who reached the peak. Being fully merged with his/her suit and helmet, and having engineered (hehe) themselves to be bigger, stronger, and more physically imposing, the individual went on a mission with the xenomorph eggs. Whatever the mission was, it failed, and the engineer crashed on LV-426, and sent out the beacon as a warning for others not to come to the planet. As the centuries passed, the engineer's bio-suit, being partially mechanical, fossilized.
And so, in Alien, Dallas and the others discover one of the few Engineers who made the complete transition to biomechanical being, who transformed themselves into a god that dwarfed humans.
The black goo comes from the Engineers' creator, and the whole film is one big damn Christian allegory
So, after hours of internet trawling, this troper found this video, which alongside explaining just about every question in the movie, notes that the movie liberally borrows biblical themes. Shaw has an immaculate birth on xmas using tech from humanity's creators, and this is reflected in the crucifixion pose of the xenomorph in the head room (and the religious murals there, too). Since the Holy Spirit (basically God himself) is what impregnates Mary in the first place, it stands to reason in this context that the black goo comes from the "God" in Prometheus, the Engineers' creator, with the Engineers equating to dark angels (as Scott has referenced them multiple times in interviews).
There was a xenomorph outbreak on LV-223 roughly 2000 years ago, and an infected refugee from this crash landed on LV-426, creating the Space Jockey crash site the Nostromo finds there
This explains why all the Engineers in the pile of bodies have chest holes (as some viewers have noted), why the human race is still extant, and why the remains on LV-426 are "nearly fossilised".
The Engineers harvested the black goo from the facehuggers
The Aliens are a species native to the Engineer homeworld, a species the Engineers tampered with, producing the lifeforms we're familiar with. They noticed that the form of the Alien that's created varies depending on the host and discovered that instead of laying eggs in the hosts the facehuggers actually deposit a dose of the black goo, spiked with it's own DNA, which causes the host to grow a mutated version of itself which violently exists the host once it can survive on it's own. The Engineers studied the black goo, learned how to either remove the facehugger conaminate or at leats make it dormant and use it to mutate bio-weapons. In it's altered state it lacks a guide for what to change the infected into so the results end up somewhat random, though Alienlike mutations are frequent, especially in simple lifeforms.
Ellen Ripley has been connected to the Xenomorphs all her life
Shaw was her great aunt or some other near relation (since Shaw was barren, Ripley can't be her direct descendant). Shaw birthed the proto-facehugger which then spawned the proto-xenomorph, setting into motion the long battle against the species Ripley would later endure.
The Predators purchased a planet of Xenomorphs from the Engineers
The Predators paid a hefty fee for the Engineers to terraform a planet into a good hunting ground. The project was due 2000 years ago, but something went wrong. The Predators were angry, and hunted some Engineers as revenge, hence the helm seen on the trophey wall in AVP:R. They've been hunting humans as a consolation ever since. When the Engineer wakes up in Promethius, he's angry because he realizes the sale wasn't completed, and takes it out on the Weyland and the crew.
Vickers is either a replicant or she was android created in a similar manner
Regardless of whether you believed the early rumors that Blade Runner and Alien were in some way going to be connected by Prometheus and its sequels, this is still not an entirely impossible achievement.
It has been established in the Alien movies that androids can in fact be programmed to act human. Ash and Call both acted human convincingly until some injury (being hit over the head with a fire extinguisher, and getting shot in the stomach, respectively) unwittingly exposed their inner workings. Even Bishop and David, both of whom were known to be androids from the start, still acted as though they were actually human in order for their co-workers to be more comfortable talking to it (hence details like Bishop eating human food, and David putting on the spacesuit even though he wouldn't need it). Additionally the corporations that built these creations would be probably have the means to falsify records in order to avoid drawing suspicion toward these people seemingly appearing out of nowhere.
The idea I'm suggesting (and the reason I cite the Blade Runner connection), is that Vickers could have been designed in a similar manner to Rachael, who was an artificially created replicant programmed to think she was human, even being given an elaborate series of false memories that make up a sort of "backstory" that she she believes to be true. Theoretically, a similar method could have been used for Vickers. Whether she's a replicant or an android, my theory is that Weyland programmed her so that she did not know this. In essence, he created her and provided an elaborate backstory so that she thought she actually was his daughter. This would explain her continued resentment towards Weyland (who never really accepted her because she was a robot) despite continuing to serve him (as she is subconsciously programmed to do so).
The human race was created for..
experiment from the Architects to cure their boldness. Someone pointed out that the robot David dyed his roots(therefor he has artificial scalp). When the Architects sees that humans abused their mighty power in robots he decided to kill them all.
The Engineer found in the pyramid is an android.
That is why he seems to be merged seamlessly with his bio-suit, while the Sacrificial Engineer had a normal body. He was like David, looked down upon and mocked by his creators, so he got mad and unleashed the pathogen, killing them all. It also explains how he was able to travel from his crashed ship to the life boat in the toxic atmosphere, without any sort of breathing device.
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