After watching the movie several times, I realized that the quest for origin has always been the quest for ourselves. That said, this is how I arrived at my hypothesis.
So much theology is embedded into this story that it clouds reasoning by distracting the thinker into relating to mythology as some kind of proof that our ancestors experienced these giant humans. Remember David and Goliath? Goliath was supposed to have come from a place where giants lived. Similar to these Human giant engineers.
The Greeks mention the Titans. As they point out (in the movie) in the archeological finds many people from all over the globe have similar accounts with giant humans. Mythology, theology, technology.
Let's forget for a moment about these continuos issues through out the movie. The existential aspects of who is our god if indeed a god made us and could we also make something else altogether subsequently becoming god to whatever we create.
This is where my theory begins.
In The first sequence where the Engineer drinks the genetic-sequencing-disruption-catalyst (black substance), he is being punished for something. He is destroyed down to the molecular level. What does this mean and where does this take place? At the most often picked location for spiritual enhancement, near a body of water with an incredible view.
The bowl containing the catalyst looked like something used in religious rituals. Much like a challis or holy receptacle. The liquid was not something good he did not expect to be dissolved as he stood he looked shocked and scared. Probably lasted long because of the fitness level. Could this be a way to seed a planet? I would think it would take more than a few million engineers dissolving in water for even some seeding if this was possible . However I think he was following some kind of ritual or punishment.
Why would he be punished and why would we care as a viewer? He is being punished for something big. How did the xenomorph come to be in the first place? It is a type of parasite that gets implanted inside a viable host. Like the wasp parasite that deposits it's eggs inside the wasp and then they hatch and eat their way out of the wasp killing it emerging as worms, which later mutate into the same insect that goes around infecting with parasites.
We can observe virtual evolution in metamorphosis. For someone to invent or design and refine this process, it would not be possible because of time constraints. So they did not make us or insects. Could they have visited earth and inseminated primates and we were the outcome? That option is viable but cruel since it would seem they mixed with apes to come up with us so we could become hosts to their xenomorph bio weapons. Why not just use pure apes? It requires a human host as we have seen.
So the engineers primed earth with people just to be hosts? Sounds like a hefty weapon with thousands of years in the planning. They must have figured out they needed human hosts and they did not want to be the hosts. They must have had a very difficult time containing the breeding xenomorphs they had, a weapon so destructive they could not control.
How did they find the creature "Face-hugger" that implants the parasite that turns into a xenomorph? It was possibly a native to the area in the form of a very small worm that when exposed to the melting catalyst grew into large one like the one that attacked them and sprayed acid blood when it was lacerated. It's head phallic in structure seemed to be made to fit inside a human mouth. This worm is the organism that was implanted by Dr Holloway when he has sex with Dr. Shaw. Those things were swimming in his eyeballs so likely swam along with the sperm and that is how that one got implanted.
It apparently did not die in the OR mobile Unit grows very fast into a giant face-hugger and unintentionally saves his host Dr Shaw from the crazy engineer. He seemed rather shocked to meet something stronger than him. The best part was the deep throat action and again we see the proboscis looks phallic in structure just big enough to penetrate a human mouth.
Why bother to go kill her after the crash? It would seem they understood English and DR Shaw asked why they were planning to unleash this on earth if they created humans on earth (by mixing with apes.) This made the engineer realize humans had advanced quite a long way in technology and could pose a threat in their plans of a xenomorph colony on earth using earth humans as hosts. He knew there were more ships but had to get rid of the problematic human. Maybe if he were to be found out he may have to end up like the one in the opening sequence.
However he gets implanted with a xenomorph parasite and it is born out of him . That leaves a live xenomorph with 2 years of supplies in the life pod. Maybe in that time he/she becomes hermaphrodite and starts it's own colony of face huggers who will await the next to visit.
If the engineers are human, then humans are the creators of the xenomorph. Who created Humans? A catalyst and time.
