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The space jockey in the very beginning commits suicide because he has been stranded with malfunctioning biological weaponry created to destroy the human race, a race they genetically engineered. This biological weaponry is out of control and killing the space jockeys in terrible ways. Archeologists discover many ancient artifacts and relics throughout various cultures that depict the origins of our creators to be in the system of planets that the space jockeys are using to create their biological weaponry. An expedition goes underway and scientist come across some sort of a microbial black ooze and other substance in vases that eventually contribute to the creation of an evolutionary prototype of the face huggers (from Alien) when fused with a human. Apparently this black ooze is what the space jockeys have been engineering on the planet and when it comes into contact with another life form, it fuses to create something quite ghastly. Example, the black ooze merging with the worms (this is slightly ambiguous but they showed those earth worm things for a reason) which caused the death of the two geologists who were stranded. The thousand year old black mural depicting the traditional alien we all know and love, and the fact that the dead engineers had burst chests, infer that the aliens are out there; a result of biological weaponry engineering and that black ooze. The engineers were perhaps experimenting with them, or trying to recreate them. Now when the black ooze merged with a human it drove them mad and through sexual reproduction creates a primitive form of the face hugger. When the face hugger merged with the space jockey it created a Xenomorph prototype. Basically, engineered microbial substance from vase + human + plus sexual reproduction = primitive face hugger. Primitive face hugger + space jockey = primitive Xenomorph. The Xenomorhps we know and love are both a product of biological engineering by the space jockeys and evolutionary adaptation. We don't see the exact aliens from the Alien franchise but we see their evolutionary ancestors and how they were created. The end. HOW DID YOU NOT UNDERSTAND THIS PEOPLE??!!!
As far as questions such as, "Where are the space jockeys from?" "What about that specific space jockeyship that was in "Alien", where is that?" For me those questions don't matter because the film stated that there was more than one ship on the planet and those ships can easily be hosting another space jockey. Honestly I could care less because all my bigger questions were answered about the space jockeys and the alien as a whole and I really don't care too much about that exact specific ship that was seen in Alien.
"Why did the space jockeys change their minds about the human race?" Just turn on your local news channel, you'll see why! It's ambiguous and it's supposed to be. The filmmakers want you to reflect on some of the themes presented and I thought that was great! It was awesome how the film doesn't give you all the answers. That's what made some of greatest films. That's what made Alien, Blade Runner, Inception, and Children of Men so great. This is one of those films people are going to watch over and over and keep finding new things in it every time...kinda like a couple of other movies buy this guy named Ridley. Thank you Ridley. Thank you for more poetry on celluloid.