Hmm, thoughts on this (AU) backstory for a 40k fic?
Ye Olde Days:
8000 BC, the Emperor is born/created.
8000 BC to around 1950 AD: The Emperor spends the next several thousand years mastering his abilities, learning random shit, and generally just fucking around. Whether fucking around means being an Egyptian Pharaoh, a Roman General, a barbarian warlord, a trader, etc. depended entirely upon his mood of the day. During this period of fucking around, the Void Dragon emerges from a Webway point around 1000 AD or so and the Emperor manages to defeat it (this is also when the Emperor first learns of the webway, and it is his explorations of that and knowledge stolen from the Void Dragon that lets him visit Mars and imprison the void dragon there). The Emperor also makes a few acquaintances of a perpetual nature, including Malcador and Alivia, during those millenia of fucking around.
While Alivia was already fairly old at the time (a thousand or so) of their introduction, Malcador was born around 1900 and the Emperor came across him shortly (very shortly) after his birth.
1950+: When humanity develops nuclear and biological weapons they gain the ability to actually wipe themselves out and so the Emperor becomes a bit more proactive in trying to protect humanity. As part of that plan, he creates the Sigillite Order and tasks them with preserving history.
Most of the Cold War and 21st centuries were spent by the Emperor playing spy and assassin while subtly trying to push humanity into space (it being much harder for them to be wiped out if they have viable offworld populations). This is where Malcador gets his predilection for assassination, intrigue, and espionage (as it is basically his childhood and the Emperor was a big believer in take your child to work day).
3000 AD/M3: By this point humanity in Sol is pretty much at an idyllic height. O'Neill cylinders populate the Sol system, power is virtually limitless, life extension treatments have been developed, direct neural interfaces are a thing, automated infrastructure takes care of virtually any physical need, etc. Psykers became an acknowledged, if incredibly rare thing around 2800 and by the early centuries of M3 the genetic basis of psychic potential had been discovered and was written into the human genome on a near universal scale as part of the genetic engineering that was utterly common.
Every human born then was massively genetically enhanced.
Study of psykers lead to the Warp's existence being initially theorized.
4000 to 5000 AD: The Emperor spends most of this exploring the galaxy via the webway and gains a great deal of knowledge about souls, the warp, and psykers. Often by stealing it from the Eldar and/or other xenos.
5000 - 15000 AD: The Emperor is now fully aware that the galaxy is a dangerous place and that humanity could be wiped out at any time by any number of alien forces. He comes to the conclusion that humanity must be spread far and wide across the galaxy. He uses the genetics knowledge of humanity and the warp knowledge that he acquired to create the first of the Custodes (the Men of Gold) and with their aid creates the "Men of Stone". The Men of Stone are essentially automated terraforming and infrastructure construction ships, they are also the first servitors as the Emperor ties psykers body and soul to the vessels so that he can communicate with (and control) them across the galaxy.
The Men of Stone head off slower than light to start preparing the galaxy for human habitation.
The Men of Iron were the workforce (and guardians) created by the Men of Stone when they arrived at their destinations. Unlike the Men of Stone, they were wholly artificial and could only be controlled by the Emperor second hand; he was also unable to keep a close eye on their creation. The Ruinous powers used the psyker nature of the Men of Stone to very subtly corrupt the code of the Men of Iron at this point of their initial creation.
Over time, slow boat colonization of all types (generational ships, genetic samples and artificial wombs, cryostorage) spread humanity across the stars but there was no real means for them to communicate with one another. The Emperor would sneak the odd Custodes aboard the various colonization efforts and he could keep in contact with them psychically but no one save his own people knew about that.
M18: The first Warp drive has just been invented. Slow by modern standards (it was basically the same model as what the Tau use), it was still fast enough to allow humanity to begin to unify and create at least small to moderate sized interstellar empires. Humanity comes to the attention of the Eldar and they take amusement from fucking with (and torturing) humanity and, with the knowledge of humanity having spread across a great many worlds, the Eldar begin using the webway to really fuck with humanity on a species wide scale.
The Emperor finds that to be utterly intolerable and uses his knowledge to create the Navigators and improve Warp drives. He also uses the same idea as the Men of Stone to create a psyker/severitor based interstellar communications network.
The Emperor carries out the first human unification and creates the Terran Federation. The Emperor's role in this, or that he orchestrated the whole thing, is known only to his own close associates.
M18 - M22: The Terran Federation makes fairly rapid advances in warp related technology. Including the invention of computers that use warp effects to be acausal in nature, dump waste energy, and gain power. This is the period when machine spirits actually truly become a thing as human technology becomes, almost wholesale, partially warp based.
This advancing knowledge, and the fact that virtually the entirety of the Terran Federation's military and civilian assets/infrastructure were networked into one massive, decentralized, AI hive mind that the Emperor could control (he controlled the Men of Stone who in turn had admin access to all of the Men of Iron and through them virtually every bit of human tech) allowed humanity to fight the Eldar (at least the ones not tied up in torture orgies) pretty much to a standstill. This was a great affront to the Eldar and so they decided to murder fuck a new Warp god into existence to teach humanity their place (the Eldar being fully aware that creating new warp gods caused warp storms and the more powerful the god, the more numerous (and more powerful) the warp storms would be. Essentially, the Eldar were planning on doing a galaxy wide "Warp EMP" to wipe out the whole human tech base.
M23-M25: As a side effect of the Eldar agitating the warp, the number of psykers being born (and their power) increases by orders of magnitude. Said psykers are also mentally affected by the emotional taint the Eldar are spewing into the warp in their creation of Slaanesh. Basically, more psykers, more powerful psykers, and said psykers essentially have proto-Slaanesh in their brains constantly telling them to act on ever pleasurable impulse they may have. Then Men of Iron become more focused on internal policing and the psykers start psychically manipulating humanities warp based tech to their own advantage.
That, along with the corruption that got into the core programming of the Men of Iron, causes them to go rogue. The Cybernetic Result lasted only a matter of minutes but it killed more than 95% of the human population across the entire breadth of the galaxy in that time period. It ended when the Emperor sacrificed all of his Custodes (the Men of Gold) and used his connection to the Men of Stone to eradicate the entire entire communications network and everything Men of Iron related.
The Eldar also used that large scale death as the finale of their creation of Slaanesh and so the feather in the cap of humanity was that safe FTL travel was now a thing of the past as well.
M25-M30: The scattered survivors of humanity are suddenly befrit of technology and thrown back into the stone age. Religion comes back and the agitation of the Warp results in even more psy related phenomena. This means that warp related religions become incredibly prevalent. The Emperor and a handful of his agents (Malcador, for example) have methods of traveling between worlds (although the webway is a great deal more dangerous than it used to be) and can even forcibly calm the warp temporarily so as to allow a ship that they are on to travel safely.
They create, and spread, STC's across the galaxy but while they do what they can to preserve/help humanity the truth is that there is very little that they can do. Especially not when the Warp is now populated by incredibly powerful entities that are hostile to humanity and basically utterly anathema to the materium (this is when the Emperor becomes aware of the Chaos Gods as actual, conscious, things and discrete entities).
The Emperor finds an Old One lab related to the creation of warp entities, genetic engineering, and soul manipulation in his quest to find a solution. This is the warp rift on Moloch. It is here that he gains the knowledge needed to create the Primarchs, and when he leaves he asks Alivia to guard it from anyone else.
The Emperor creates the Primarchs after a millennia or so of concerted effort. The Ruinous Powers use the fact that some will become corrupted in the future to reach into the past and toss the lot of them across the galaxy. Where they arrive is mostly a matter of warp resonance across time; they arrived there because everyone in the future knew that they arrived there and they were shaped by the beliefs of humanity in them.
Magus, for example, was a red cyclops because countless trillions of people knew that Magus was a red cyclops.
With the Primarchs thrown across the Galaxy, the Emperor decides that he needs to greatly accelerate his plans as he can't afford to allow them to all independently do what they were programmed to do (conquer the galaxy). If he left them on their own then inevitably they would each be at the head of their own empire and war on one another, and the Emperor, when they eventually came in contact.
M30-M31: He creates the Thunder Warriors as his tool to conquer Terra and a test run of several ideas. Then he uses refinements on that process to create the Space Marines and, as a result of how they are created, kinda sorta soul bonds them to their primarchs. Largely to the same extent that the primarchs are soul bound to the Emperor.
Basically the Great Crusade/Horus Heresy.
Malcador and the Emperor wipe the Lost Primarchs from all record and memory in an attempt to alter the past. If they are unknown then the psychic weight behind them is lessened a great deal and the Emperor can use his own power to tweak where the Lost Primarchs arrive.
If the Emperor actually dies then he uses the power of his death (and the disruptions that it causes both forward and backwards in time) to tweak those arrival points. It is his final contingency plan and he will keep replaying history until he gets a result that is more satisfactory.