This is my theory on the origins of the Emperor. Us 40K fans endlessly speculate on where the Emperor was in our history, and who in history the Emperor may have been. To me the answer has always been pretty apparent that a being of such power, and the 'Shamans' would show up in our history and be very noticeable. The Emperor was born in Anatolia in 8,000 BC an it seem to me the only real records from that time are later recordings of myths and gods.
The Titans of Greek Myth seem to be very elemental, like 'time' and 'chaos'. Translated in 40K I suspect they would turn out to be the Old Ones, or the Slann (agents of the old Ones, though I think the various monsters could actually be the 'Slann' but demonised for the myths - like the Cyclops or Hydra).
Gods (real gods)
I propose that the Gods of antiquity where actually alpha-class psykers of immense power that gave rise to Greek myths of the gods we read about in the great sagas. These Gods are the progenitors of all humans. However humans as we know them today are a degenerate offspring of the Gods (think Hesiod's Five Ages). It seems alpha+alpha does not equal alpha offspring! The first generation are demi-god, so originally there are demi-gods and all sort running about, which gives rise to lesser demi-gods, but it all boils down to modern humans (with no powers to speak of). Every now and then a new psyker is made (throw back) and even new alpha-class psykers emerge.
According to the legend of Titanomachy the Titans and Gods have a bit of a war and things get messy. So in this concept the alpha psykers have a war with the Old Ones, or perhaps more specifically they may have had a war with the Old One's agents: the Slann. Then they probably close the web way gate on Earth (the one the Emperor 'found').
Further to this concept: The Emperor, for some reason or another, consumes the other gods (as Greek gods tend to do in the myths) and contains all the other god's 'souls' of that age (which gives an alternate version of events to the Shaman sacrifice but matches the same outcome of a 'gestalt soul'). When creating the Primarchs he literally plucked them out of his being and bound them to a clone body (clones are supported by some of the background). They came out different because such a powerful soul would have an effect on the body (plus a little chaos influence). The Emperor can not make new super souls, but he can make clone bodies.
I would say the Emperor is 'Zeus' / 'Jupiter', the last god standing. This gave rise to the monotheistic and monistic religions in ancient 40K, the first real version being Aten. I can see the Emperor, bathed in golden light and with a halo as a version on Aten.
Anyway, the Emperor is the king on the gods, consumes the other gods to become one god. Then vomits up (god seem to do that from time to time) a whole bunch of gods he had previously consumed and bound them to clone bodies. The betrayal of the Primarch may have more to do with ancient history than chaos.
In this little pet theory of mine is about magic and gods in the old fashions sense. There is not high tech alien influence, and not technology fossils. The reason being that god like powers kinda negates the need for technology, or if you have psionic powers to the point of a 'god' (in the Greek god sense) you really do not need technology. Therefore there would be relatively little technology during the era of the gods, and all technology is most likely invented by humans over generations as they lost their powers (or relied on 'god' to sort it out, which back then was kinda like asking great-great-grandfather to sort it out).
Then the Primarch are recreations of past 'gods' and would be (technically - if true) human. They would be part of the Homo line, before Homo sapiens (sub-species sapiens). This particular human is totally missing from the scientific line as we know it – as they have not 'died' and left remains. The Primarchs would be as human as the Emperor is human, but they are not post-(modern)human but pre-(modern)human. I suspect they are merely a version of human who has been genetically tampered with (but still compatible with humans) and more a sub-species. Basically the greatest of genetic traits blended to a form of 'perfection' (in a gross all out warbot kinda way).
Looking at the old myths, it seems the children of the gods become minor gods with far less power, and the children of the minor gods are weaker still. After several generations (or hundreds of generations) the offspring are literally plain old humans with not super psyker powers, though we retain our smarts and 'soul'. The other problem is that at some point we do not have the powers to rejuvenate, and we are no longer sustained by warp energy and we became mortal.
In this scenario a demi-god isn't really a demi-god, but a mating between earlier generation with a later generation of human. This may boost the child's power compared to the generation of a given era, and elevates them above other humans, but they will not live forever.
All the evolution of mankind could be Slann interference (though probably not due to the time line), or some other interference. I tend to see the human experiment as a 'failure' as it can't give rise to new super powerful souls with any regularity, and most (back in the day) I would guess had to be artificially created and bonded to a human body (possession?). The body and mind reproduced properly in off spring but the soul did not generate correctly (incompatible souls? Not 'soul mates') and degenerated in power over successive generations to become weak and eventual un-psyker (this engineered link to a powerful soul is probably why daemons can possess a human - as all the plumbing is there)
But things did not go smoothly with the Gods (Psykers) and Titans (Slann?). The Emperor (Zeus) as one of the old Greek Gods (not a Titan) eventually gets into a spat with the Titans which is 'oh so human'. I would guess this is what happens when you build a super-weapon like a alpha-class psyker - your creation may decide that they don't need you! It is a fear that humans have of their creations, because it's exactly what we would do (and in this case did). We project our power lust onto everything to form targets and then seek to tear it down in the name of self defense.
Humans are very destructive - we are made that way! We are designed (in 40K myth via Philverse) to destroy everything that is not human, and have an engineered fear of the unknown and those not like us (hit it first and ask questions later). We stay ever vigilant, and are always up to no good. Sometimes this Old One/ Slann engineered imperative goes astray and we demonised other humans, but all humans when confronted by real aliens become 'adjusted' or 'synchronised' to the target and rally together.
Eventually the Gods realize humans are a lost cause and will continue to degenerate, their reliance on technology will make them weaker and weaker; eventually forcing them to tamper with their own genetics. This tampering will make humans incompatible with the last vestiges of the divinity, and sever the soul link. They become automatons, devoid of creativity and passion, the fire in their eyes finally goes out and they eventually loose the will to live.
Unless someone does something about it - cue the Emperor and his amazing powers of interference on the sly (and the web way, nothing like having super powers 'gods' charging about the web way causing trouble for all! oh, and these god may have been around for a long time, they may even be the Eldar gods too!).
Also chaos may be closely linked to humans (there are a lot of them all over the place) and with the 'current' lack of our ability to draw power from the warp it may be creating a backlog. It may be that humans in 40K do not feed the warp, or the chaos gods, at all. It may be a case of 'flow of creation', and the Old Ones may be unable to channel power though humans to work their wonders (like they could with the Slann - which we may have killed). All this backlog of creative power may create the chaos gods which then cause trouble. The chaos powers or daemons can possess a humans in a temporary way, but this is due to weakness in the humans but the link still existing.
It's all a huge mess, but great fun! (well, I think so, but I would - wouldn't I) Again it's all down to how you imagineer it, and this musing can be as wrong or right as you like it.
PS: This has been used as a base for the Of Ghods and Primarchs on my site.
Hearing feedback is very important to me in developing my ideas. Much of my designs are inspired, and crafted, by chatting to fans on forums before snowballing into a full concept you'll find here. I would like to thank all those who have contributed critiques and participated in discussions over the years, and I would especially like to thank all those who commented on this specific topic. If you would like join in, you are most welcome!
To support my work: Connect