SPOILERS
Right this the a I've tried to explain so of what I saw last night, a fine indication of the way my mind works, or a pure sign that I think too much...
As mentioned previously when I looked at Prometheus as something with a bit more depth, loads of questions began presenting themselves, and some observations that spoke of how badly constructed the script was, or perhaps to be more honest how badly thought out the script was.
One of the things I kept thinking about though was the film being a prequel of sort to Alien, and how does it all fit together when there is not really an appearance by any particular part of the Alien creature, just things that seem familiar.
This is what I have come up with, and I just wondered whether it makes sense, and connects it properly with Alien.
At the start of the movie we see something happening in, presumably the distant past on Earth. One of the un-helmeted Engineers consumes a substance that affects him on a genetic level, causing his body to break up and dissolve into the planets ecosystem. This spreads outwards, altering the course of evolution, so the dominant lifeform becomes, if not the Engineers, something that is certainly genetically related. (As an aside is it possible that the Engineers engineered the extinction of the Dinosaurs in order to make way for their own progeny?)
Back in the modern day we get to see the Engineers running away from something. We have no idea when this happened, only that it was in the past – and if it was enough to make the Engineers run, it must have been something powerful.
Although the catacombs seem to have no life there are sporadic readings, and it seems to have a snake like creature that lives in the black goop. This turns out to be aggressive, close to lethal and when wounded bleeds acid – the first direct link to the classic Aliens, although nothing like them. It also goes straight for the mouth and worms its way inside the hapless scientist – again something comparable to the facehugger forcing an egg into its host, only the full creature goes in. We have no way of knowing what happens next as we never see him again.
Later the android David takes a sample of the black fluid and contaminates Holloway’s food, and later when he sleeps with Shaw he impregnates her (even though she is barren) and she starts gestating at a highly accelerated rate. (Again although nothing like the original Alien, it too grewat an exceptional rate).
When the ‘baby’ is removed it is certainly not human, looking more like a squid. We don’t see it again until it attacks a re-awakened Engineer, but when we do see it, it has grown to giant proportions, easily big enough to overcome the Engineer, which it does by forcing a tube down its mouth. The creature looks like a giant facehugger.
Later the Engineer is ripped apart from within, and something that has some similarities to one of the classic aliens emerges. Different, but recognisable.
The only other fact we are presented with which is important to my thought process, is that the Engineers have apparently decided to wipe us out, and by the end of the film we do not know why.
Right, now this is where I attempt to string this all together:
In their time the Engineers were one of the most advanced forms of life in the Universe. For whatever reason they saw it as part of their mission to make their type of life the most dominant in their Galaxy and travelled to countless world seeding them in a manner that meant the most dominant life form was based on their genome.
As stated the way this was done was to dissolve their genetic structure into the planets ecosystem. This was done using a rather painful method that was started by taking a small amount of a black goop.
I'm going to guess that this 'goop' is some kind of artificial biological compound that interacts with physical life forms, not only breaking it down but connecting to new forms and aggressively altering it to become the dominant force, setting in motions that persuade evolutionary paths to follow the ones that lead that planet's species to become as close as they can to the Engineers.
At some point in their countless travels the Engineers picked up a parasite, which was accidently carried into their main supply of goop. Instead of dying, the parasite, which was particularly aggressive adapted to the goop, and its DNA began to evolve at an unprecedented rate. The parasite grew into creature that adapted to become the most perfect hunter of whatever dominant species was nearby, in this case the Engineers.
As it became apparent that the new lifeform was evolving to deal with any threat the Engineers might have become they were wiped out... hence the stampede as a supremely powerful species found something they could not control.
With its connection to the goop the lifeform continued to adapt, becoming the most pure form of what it was: a lethal killer whose biological imperative was to destroy.
When it comes into contact with humans it begins to evolve again, it's gestation in Shaw allows it evolve into something that will better deal with humans, but taking on the most lethal traits from the parasite, the Engineers and humanity.
Thus following through the human gestation cycle (at an enhanced rate) it developed a process that it could inseminate the human (facehugger) and emerge as a rapidly growing deadly creature.
Because the Engineer was bigger it came out larger than it would from a human, but recognizably as a proto-Alien. A little refining and the Alien's would be happily waiting for the Nostromo years later - especially if the 'Alien' we saw at the end was a Queen, ready to start laying eggs (or did the canisters get changed or used in the first instance).
And why do the Engineers want to kill humanity?
Perhaps Earth is where the virus that became the biggest threat they ever faced came from...