Many were the voices that gave praise to the Emperor, that called him divine, godlike. During the Reunification of Terra and further into the Great Crusade the Emperor denied such claims. He would lead humanity from the superstitious darkness of Old Night into a new age of enlightenment, a golden age for humanity. The Imperium of Mankind, an empire built on reason and securing and safe guarding humanities' place in a hostile galaxy.
At some point the Emperor stopped denying claims of his divinity. It is unclear why this is the case, perhaps the Emperor simply tired of it; perhaps he sought to embrace the Immaterium and the power he know that lurked there; perhaps he simply traded reason for madness we may never know. What ever the cause the effects became clear. The XVIIth, the Word Bearers, ever idolators, were the most vocal Legion claiming the Emperor's divinity. Each world they brought into the fold of the new Imperium they would make sure was utterly loyal, utterly faithful to their God-Emperor. Worship of the Emperor spread through the Legions, slowly at first but growing at an ever increasing pace.
Not all the Legions developed the same levels of faith in the Emperor. The XIIIth, the Ultramarines and XVth, the Thousand Sons under the reasoned gaze of their respective Primarchs clung to reason as more and more of their fellow Legions developed a greater degree of faith in the Emperor. These Legions were by no means untouched by faith, especially when compared to their brother Legions.
When the Emperor declared Guilliman as Warmaster he took the opportunity to begin his Great Work. What this was is unknown, however it coincides with the reintroduction of the Word Bearers Old Gods amongst the Legions and the populations they conquered. Rumours began that the Emperor's great work was to indeed attain Godhood. The wisest amongst humanity began to worry what this might mean for the nascent Imperium, built as it was on the ideals for throwing off the shackles of superstition.
A darkness was spreading through some of the Legions. The White Scars became ever increasingly fulled by rage. Giving up on their old hit and run style of warfare to simply plow into the enemy and inflict as much carnage as possible. The Iron Hands who had always sought ancient and forbidden technologies and knowledge, began using and unleashing and unleashing to forbidden powers they had come in possession of. The Night Lords ever the masters of moral destroying warfare, came into their own when the Emperor praised their efforts. They began to bring greater woes upon their victims, destroying and corrupting food stores, wiping out more with plague and famine than with bolter shells. Lastly the World Eaters who although consumed by rage found an almost endless pleasure in the mad butchery they unleashed. They would continue battles well beyond their reasonable ends and hauled scores of prisoners off to their arenas so they could satiate their battle lust when there was no battle on offer.
(summary with some added details)
-The Emperor stops denying his godliness during the Great Crusade.
-The Word Bearers having never been rebuked for spreading the word of the Emperor sway many of the Legions into worshiping him as a God. All worlds they conquer are set up as shrines to the Emperor.
-The Word Bearers reintroduce worship of the Old Gods, this also spreads through the Legions, if at a much slower pace.
-Rumours abound that the Emperor's Great Work is an attempt to become a God. This worries several Primarchs, notably Guilliman and Magnus
-Unlike in the canon the World Eaters, Emperor's Children, Death Guard and Thousand Sons never turn to Khorne, Slaanesh, Nurgle or Tzeentch respectively.
-The seeds are sown for the White Scars to follow Khorne; the World Eaters to follow Slaanesh; the Night Lords to follow Nurgle and the Iron Hands to follow Tzeentch.
Notable events of the Great Crusade.