'kay.
So y'know how the accepted origin story of the Emperor is that a bunch of psyker shamans did mass suicide and fused into one giant soul? In my headcanon, that wasn't what happened. Well, it did, but not for him.
The shaman combination soul thing did happen, and it formed a combined superpowerful immortal psyker, who over the eons was such esteemed figures as Jesus, Buddha, and Mr. Rogers. Sometime in the 30th millennium, this being was known as Malcador.
He did the stuff that the Emperor did in canon pre-age of strife, stayed in the shadows, tried to positively influence humanity subtly, etc. For a while it worked - the Dark Age of Technology came about, humanity was the second most powerful species in the galaxy behind the Eldar, at the time the unstoppable galactic hyperpower, Heirs of the Old Ones, etc. Then the Age of Strife happened and Malcador, knowing about chaos from his 27,000something years in existence, knew shit was about to go down and sensed that humanity was about to get its shit kicked in even harder than it was against the Men of Iron, which they barely won against by deploying technology inspired by the thoughts of the sleeping Void Dragon on mars. So he decided he had to take drastic action - humanity needed a leader, a shining beacon to guide them through the dark times to come. But who? He could give it a go, but he was a humble dude and didn't consider himself powerful enough for the task, especially given all the threats that'd try to shank him should he try. So he decided to do something else.
Humanity remained fairly religious even well into the Dark Age - the sheer fact of having a soul renders a species instinctively wanting gods or a belief system, an ideal to aspire towards. The most successful religions were stuff from the most dominant on earth right now - Christianity, Judaism, islam, Buddhism, stuff like that. Altered by time obviously, but the same basic tenets. All that belief accumulating over the millennia eventually would've formed a warp god kinda akin in function to Asuryan and the rest of the Eldar, protecting the species from Chaos and all that stuff. It takes a critical mass of accumulated belief to make a god though, and it wasn't quite at that point yet by the time all the warpstorms came about. It was just kinda sitting there in the warp, begging to be used.
In a ritual reminiscent of the process that formed him, and long before, some things the Old Ones did, Malcador used all that belief and coalesced it into a soul. A newborn fully grown as a man. The Emperor of Mankind.
The Emperor was aware of his nature as a godmortal from the moment of his birth, and forever in conflict because of it. He possessed the capacity to basically blow up planets, annihilate anyone that stood in his way if he so wished - he was a god concentrated into the form of a coherent soul, allowing him to focus all his might into one vessel. But it came with a cost - whenever he tapped into his powers other than his passive use of it, which is the super-charisma, his 'godly' side grew more dominant over his human side. His godly side is basically all the weird controlling asshole things he did in canon - the Lorgar overreaction, teleporting Angron up without his buds, never telling anyone the fuck he was doing, etc. The human side of him is the more reasonable depiction of him. It was forever a struggle for him, and the more he used his powers the stronger his asshole god side grew. As he grew as a person, he became disgusted by this side of him and vowed never to succumb to it, hence his militant atheism despite the fact that he clearly knows better and his pushing of the Imperial Truth.
To avoid having to expend too much power and thus let the god side overwhelm him, he decided he had to create generals to help him on his crusade to unite humans. To that end, he took various minor gods/saints/etc still worshiped and remembered and made them into people as well, creating the primarchs. Leman Russ was Thor, for example, and Sanguinous was St. Michael.
The crusade went well at first, he didn't have to do too much in the godly might department and he was gonna make the Imperial Webway to stop his having to project the Astronomicon. Then Heresy of the Horus variety, things went to shit, and he's stuck on the Throne with people worshipping him as a god, the thing he feared most would happen.
The last ten thousand years have been an exercise in agony for the Emperor, who not only has to watch the Imperium he built with Malcador's help crumble into a bigoted theocracy, he has to experience all those desperate prayers to His might ringing out throughout the galaxy. He hears them all, and is empowered by them, and increasingly he cannot stop himself from answering. The asshole side of him has grown to dominate his being as his soul grows splintered from the effort of holding everything together, leaving his human soul - what some call the Star Child - a small nugget of decency, constantly screaming in horror as his mind gets rewritten by people who claim to love him.
He hears the asshole side whispering to him. Look at the masses, how badly they're doing things. No coherency, no vision, just strife and petty conflict. Wouldn't it be so easy to just ... take control? Do it. Take command. Direct your subjects. Make things better. Dominate them. Protect them. Oppress them. For their own good. You know you want to.
Humanity's guiding angel died forever on the golden throne 10,000 years ago, and the Emperor can feel his hold slipping as he slips ever closer to becoming a chaos god.
GRIIIIMDAARK
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