During the Great Crusade there was a set of rules that helped track a Legions loyalty to the Emperor. Thus if a Legion fought in a fashion the Emperor approved of, or towards the Emperors goals they became more loyal. This included fighting of evil Xenos hordes and being heroically outnumbered. Whilst those that used more unorthodox tactics or were more inclined to follow thier own goals had their loyalty drop. This included political and actual infighting (represented by games) or going into a fight with a ridiculous amount of resources.
This system is why some Legions, despite having events that negatively affected their loyalty still came out as very loyal. The White Scars are a perfect example. Their loyalty shot all over the place until right at the end of the campaign they managed to drag themselves through as loyal.
The tl:dr at the end will give a quicker overview and say where the differences with the canon occur. Back to the Events of the Great Crusade:
Ever indulgent to the heights of brutal carnage and bloodshed the World Eaters were reknown for their ferocity and the devastation their attacks caused. During the Great Crusade the came to enjoy their slaughter more than they previously had. The World Eaters began to take prisoner their stronger opponents, dragging them back to arenas on their mighty warships. Where once they would wreak their bloody toll as quickly as possible, they have taken to what on the surface would appear to be a greater tactical acumen. Outflanking their foes, dividing held positions and raids; all uncharacteristic of the Legion. Taking a closer look at the legionnaires it is noticeable that they are building up their anticipation for the final strike, where they glorify in the horror of the slaughter they inflict.
Willing to do whatever was needed to bring worlds to heel before the might of the Imperium the Space Wolves found themselves falling out of favour. Whilst the likes of World Eaters or White Scars would slaughter any living thing within arms reach the infrastructure of a world was largely left intact. Not so for the Space Wolves. Their willingness to use incredible collateral damage as a weapon often meant more time was spent rebuilding the shattered worlds left in their wake, than even a lengthy campaign would have cost from any other Legion.
During the Great Crusade it became known to progressively more Legions that the Blood Angels harbored some secret. Eventually it was revealed that the IXth had a flaw in their geneseed, that caused them to loose all self control and enter a dark rage and thirst for blood. The Blood Angels no longer able to contain this secret, were commanded to purge the Legion of all signs of genetaint and to cease all recruitment immediately. Knowing that this would mean certain death for the IXth Sanguinius refused the order. The Emperor's response was swift, the Blood Angels would hence forth be removed from active duty, any action counter manning this would see Imperial retribution.
Despite or possibly because of the events on Chogoris the White Scars continue to grow in favour with the Emperor. Whilst this seems to temper their combat doctrine slightly from the total slaughter that had recently become their new favoured way of war it caused a select few Legions to really focus together. Calling themselves the True Legions the White Scars, Alpha Legion, Salamanders and Dark Angels saw themselves as being above their brother Legions, an inevitable sign of the trouble that was soon to occur.
After being given some crucial intelligence by Robute Guilliman the White Scars learn that the Raven Guard have been repeatedly attacking isolated White Scars forces and disrupting their communications networks. The Raven Guard are suspected of instigating the rebellion on Chogoris as well. The Emperor, furious that one of his Primarchs would take the liberty to censure another Legion, let alone the highly favoured White Scars, declared the Raven Guard to be enemies of the Imperium and gave the White Scars the honour of ridding the Imperium of such a clearly treacherous enemy as the XIXth.
(summary with some added details)
-The World Eaters are the first Legion to start the path to following a Chaos God, in their case Slaanesh. In the cannon they obviously turned to Khorne.
-Like the Thousand Sons the Space Wolves have lost favour with the Emperor and or the other Primarchs
-The Blood Angels are ordered to purge their legion of tainted geneseed, Sanguinius refuses and his Legion is stood down, on threat of being attacked by Imperial forces. This is broadly analogous to the Word Bearer's being rebuked by the Emperor in the canon.
- The White Scars once again prove the firmness of their loyalty. This causes the most loyal Legions to band together.
-The Raven Guard are cast out of the Imperium for daring to censure the White Scars. The White Scars are then sent to destroy the wayward Legion. This is the equivalent to the events involving the Thousand Sons and Space Wolves in the cannon.