So, after a couple of days of thought, here's my complete revision of the Prometheus story.
Please bear in mind, I love Alien and Aliens, like Alien3, don't care one way or the other for any subsequent films and have never read any comics or fan fiction. I'm not a "fanboy" just someone who likes smart and well-made movies.
My 'revision' is based upon my interpretation of Giger's life cycle painting, which is just beautiful, and upon stuff from Alien about the SJs being an ancient and noble race.
The new foundation is as follows
The SJs are a humanoid (but not human) race who have a technology based around biology - they design and use other creatures to do things for them, such as acting as environmental suits, transportation. For example, the ships are living beings, and the external appearance of the SJ in Alien represents partly the body of the SJ itself but a growth of the ship's pilot chair around it. All of this engineering benign, but has had some unintended consequences. For example. they cannot help but contaminate worlds they explore (such as Earth), spawning the development of new life forms or the modifcation of existing forms.
So, I argue that the SJs led to the development of humans, but accidentally, and they've never returned so they don't know how we turned out.
Secondly, the life cycle of these being is based upon death. As a SJ nears the end of its life, it gives itself up to be impregnated by a facehugger. A creature grows inside the old SJ and the birth is assisted by SJ 'midwives' (the two guys in Giger's painting). The dying SJ cradles its new child as it passes on, and then the baby is put in a nursery to grow. What grows is NOT the xeno, but eventually an adult SJ, calm and intelligent, even disturbingly beautiful. However, they have (under those masks) slightly elongate heads and eyeless faces. This is the overarching being of the Giger painting.
So where does the xeno come from you ask? Well, the normal life cycle of SJ involves merging the DNA of the dying SJ and the facehugger. The dead SJ is then biologically reformed - coccooned - to form an egg and a new facehugger.
But, when one of these creatures grows IN A HUMAN it takes on the aggressive human traits of our race (I know, terribly racist of me). Instead of becoming a SJ it develops rapidly into a slavering vicious beast.
In the revised story, I would ditch the archeaology strand. Now, we have a survey team exploring other worlds. They come across a SJ exploration ship and engage in peaceful first contact. The android on board tries to steal their biotechnology (under orders from W-Y to obtain any advanced alien tech that's found), enlisting one of the crew to help him steal an egg. However, the crewperson gets facehugged and SJs discover the theft. To the humans' disgust, they allow the embryo to gestate, as this is a sacred thing to them. The SJs are horrified to find that what is born is not what they expected, but a monstrosity that runs amock.
Fearing that any further interaction will lead to more monstrous hybrids (since ALL their technology is biological), the SJs try to eliminate the humans, who of course fight back. We see examples of SJ tech misbehaving or growing new and malevolent variants as it interacts with our biology (our bugs and viruses). Like so many first contacts in human history, it's the tiniest bugs that can wipe out whole species.... from small beginnings.
The last survivors realise the only way to protect their homeworld is to destroy the ship. But in a climactic scene, the surviving android and last human fight to stop the last SJ from doing this and instead they have a violent (but ultimately not destructive) crash landing on LV-426. The SJ in the pilot chair is killed, the last human - flung against the wall - is dead. Only the decapitated android remains. He uses his internal transmitter to send a message home, giving the frighteningly detailed description of the aliens and alerting W-Y to the amazing biotech the SJs have. As this message is being sent, we hear the tearing and slurping noises from behind him (he can't turn his head so doesn't see - and neither do we), but there is a little screech - something rushes past and knocks the androids head off the pilot chair platform into a dark recess of the room where a part of the wall falls on it, covering it up.
The movie ends with the screech still echoing down the corridor.
