After reading and watching a lot of comments, theories, scripts, interviews and so on, I came to this theory that I think, make a lot of sense.
The first engineer we see in Prometheus are not the same as the "Space Jockey" engineers.
They are clearly a different iteration of the same species.
The first one that we see in the opening of Prometheus is almost naked, where we can compare the two different races.
From the deleted scene where we see the old engineer and some others, although they obviously are from the same race, we can observe there are some slightly differences between them.
Their faces are different, like normal humans, when you can distinguish one individual from another.
Their bodies are also very human like.
The later engineers we see in the movie, are much more alike each other, like twins. Their "suits" are not something they can undress. It's part of their bodies. It's organic, it's a exoskeleton. We can confirm this when we pay close attention to their necks, where the whole "suit" starts to "grow" from their bodies.
In my opinion, this can means only one thing: they are clones from the original engineers.
At some point in their natural evolution, they lost the ability to procreate. So, to avoid extinction, they had to find a way to pass forward their genes some how.
Then they came up somehow with the black goo we see the engineer drinking in the beginning of the movie. Although it's not the same black goo we see later one. It's clearly not entirely black, and has a different effect on the body. Sacrificing one being, but giving origin to life transmitting the donor's base DNA forward.
Looks like it was ok for a while, but they realize the time this process could take until a species could evolve was impractical. They could not be around anymore to pass their knowledge.
Also, the results were unpredictable. Depending on the planet this process could take place, innumerous variables could interfere on the resulting species. Some times not resembling at all the original engineers. Not only physically but mentally. They could become extremely violently and not share the same values.
At this point, they started to tweak the black goo. Trying to come up with a version where this variables could not influence so much.
As currently said, the biggest achievements on science came by accident.
Probably during their various attempts to improve the process, one version of the black goo gave the origin to the first facehugger, when it was drank by some engineer. Like the one that Shaw "gave birth". Which impregnated one of the them and gave the origin to the first Deacon.
At some point, the last of the original engineers have died. And with it, a big problem. There was no more original DNA to be the basis for the black goo to mix with.
So probably they used the blood from this first Deacon, as it was "born" from the one of the original engineers to continue seeding life throughout the space.
That's why they worship the big head and the Deacon one the mural in the big head room. The big head represents the first original engineer who gave "birth" to a deacon, sacrificing himself. And the first deacon, the creature who made possible, through its blood, to keep their species alive.
But it's blood was slightly different from the engineer's original blood. So, the species that came from this deacon blood, originated the new engineers with the bodies covered with the exoskeleton.
But, at some point the blood from the decon ran out too. And they started trying to replicate its blood.
Which gave origin to another type of deacon, a protomorph. That they discovered, could be used to wipe clean the life on a planet where some species could not be evolved as they expected to, and start it all over again.
One of theses species, could be humans. Although they could procreate, we started to develop beyond what they could desired or control. They tried to warn us in the past. What could happen if we not behave. "See this little planet here? That's where the doom will come from for you."
Here we could inclusive talk about the Space Jesus theory, where the engineers tried to put someone from "inside" to put some reason on humanity.
As this also didn't work, they gave up and decided to wipe the earth clean.
Now, the planet where David released the black goo.
We see they are very look a like the original engineers but are not the same. We also can see that are females between then. Probably they were the only species resulting from the process to replicate the life, started by the original engineers which paid off.
They were their favorites. That's why they were some happy when they saw the ship coming. The engineers probably visited them on a regular basis to pass on their values. And one day, they could became technologically advanced as they are now.
That's why David released the black goo one them. For him, the engineers as the humans, are dying species and he will not allow them to continue living more than he thinks, they deserve.
He believes that can create the perfect organism, one that is worthy living, breed to survive at all costs. So he decides to perfect it using Dr Shaw's DNA, because he admires her "survival instincts" as he says at one point in the movie. And want to pass this behavior to the new species he is creating.
As how the eggs get to Lv-426 in the ship that crashes there and are found by the Nostromo, I still have no idea and I hope to see a good explanation in the next movie.
I hope this theory brings more discussion and inspires more ideas about the engineers. I know it got way too long. Probably because English is not my primary language. I am certain it could be less dense somehow and made my point the same way. Sorry for that. I home it's not too confusing.
Let me know what you guys think.
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