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 Togusa wrote:

Who is to say that there is only one path? This flies in the face of the Emperors science based logic, destiny is fictitious, so there should be infinitely many paths for humanity to follow.

This is the big lie the Emperor knows he is telling. Science is only part of the picture. "Gods" exist in the form of daemons and the Chaos powers and E's plan is to cocoon humanity in the webway until it is strong enough, psychically, to fight/resist these powers. Within the context of what is explained in the context of the novels, E certainly believes that his way is the only way, and there is nothing shown to suggest otherwise. The visions presented by the Chaos gods are heavily laden with bias to a specific side, and the Kabal want humanity dead quickly to cause the chaos gods to sort of 'burn out', and need the Emperor dead for that to happen. The only option that presents anything 'positive' (and yes, thats a relative term!) for humanity is the Emperors vision. Suppression of religion is a necessary step on the way to his vision.
He knows all of this and that the "Imperial Truth" (notice how its always "the Imperial Truth", not simply the truth!) is a lie. He wants/needs worship to end as that feeds the Chaos powers.
For me, the weakness in the Emperors arguments stems from one (or more - or all!!) of several reasons.
He cant think or reason like a human because he isn't one (whether he ever truly was is a different debate)
He ultimately doesn't care. Comply or die.
He knows his own arguments are flawed and/or doesn't believe the point he is arguing.

 Togusa wrote:

Now, that part I agree with. I would like to see more stories from this time period. The massive cultural, sociological and religious changes of the time are and would be fascinating to read about. See how the emperor interacted with other warlords and the like.

You do seem to have a problem with how the Big E is written, but you're high fiving the other character in the story. The same author wrote both. This also fits into how the Heresy narrative has progressed. Starting with McNeill in Mechanicum, the books have woven the narrative that the Heresy was designed by the Emperor and that it's part of the narrow path that he is trying to make humanity walk. He doled out love unequally on purpose to stoke rivalry and cause a civil war that would see the tools he no longer needed purged from the galaxy. Now, I think that's a very lazy plot device of "all these plot holes...they're on purpose and part of a great plan!". The story to me would be better if the flaws in humanity were what caused the perfect vision to crumble.

The whole Horus Heresy was just a retelling of Paradise Lost and initially had very little written about it as it was a shrouded past for the current 40k universe. The presence of the Emperor is pretty important to satirize our world. It's a universe where a fascist theocracy is the only way for humanity to survive.