For the first year of the campaign I made a series of events to cover some of the important milestones for the Legions in the canon. The Great Crusade saw us fighting to see who had the honour of becoming Warmaster (won by Steelesamurai's Ultramarines), as such there was initially no Dark Imperium and the Emperor was the great and terrible being we all know and love.
To keep things interesting the events that turned Legions to the chaos gods did not meant that they had to turn against the Emperor. I did this because in the canon the Emperor does not seem to have really taken the threat of Chaos that seriously prior to the Heresy and no one noticed 4 Legions starting to fall to chaos.
The tl:dr at the end will give a quicker overview and say where the differences with the canon occur. On to the events:
Shortly after the Aplha Legion was reunited with their Primarch the Alpha Legion were approached by a xenos council known only as the Cabal. Nothing is known about what occurred in this meeting although rumours abound. This left the question in the air about where the Alpha Legion's loyalties may lie. Ever a secretive and unorthodox Legion the Alpha Legion gave a full account of their activities over the course of the Remembrancer Project, information they had previously suppressed. Their combat record suitably impressed the Emperor, who gave greater favour to the Alpha Legion.
The White Scars found themselves under a considerable amount of scrutiny, especially from the Raven Guard. Whilst their actions were proving ever more brutal and erratic their effectiveness could not be denied, and they found themselves bordering on censure for their actions and being a favourite of the Emperor.
The Dark Angels and Salamanders fought alongside each other for a considerable length of time forming one of the tightest bonds of brotherhood between any two Legions. The two Legions proving time and again they were both willing to give up everything for their brother Legion and the Imperium they fought for. The Lion and the Drake became one of the most popular and best chronicled accounts of any of the Legions during the Great Crusade and gave the two Legions their nicknames of the Paladins of the Imperium.
The Thousand Sons have their methods and combat doctrine called into question, along with the continuous efforts of Magnus to lobby support from his brother Primarchs, sees the Legion fall from the Emperoro's favour and begins the process that will result in the Council of Nikaea.
In one of the most notable, bloody and brief campaigns in the Great Crusade referred to as the Scourge and the Wrack demonstrated what would occur when the Death Guard and Night Lords are capable of when working together. The two Legions developed a sombre camaraderie that rivaled the Dark Angels and Salamanders.
The White Scars hear that their home world of Chogoris has thrown off the rule of the Imperium and betrayed its oaths to the Emperor and the White Scars Legion. The Whites Scars take a considerable amount of time to react and it is later assumed that this is due to the actions of the Raven Guard. Once the White Scars do react they show brutality and savagery beyond that of any other Legion. In a week of untold carnage they reduced the population of Chogoris down to a mere 0.1% of its number the week before, tens of millions slaughtered. Those that were "lucky" enough to escape the slaughter were reduced to breeding stock to provide the Legion with the recruits needed to continue.
(summary with some added details)
-The Alpha Legion follow the Emperor (instead of the Warmaster as in canon) after meeting the Cabal.
-The Alpha Legion's loyalty to the Imperium is called into question and they prove beyond any doubts that they are utterly loyal to the Emperor. In the canon this event represented Horus assuming, wrongly, that the White Scars would join him.
-The White Scars loyalty to the Emperor is unshakeable. There were several of these events that represented those Legions that were steadfast in their loyalty to the Emperor in the canon such as the Imperial Fists or Iron Hands.
-Vulkan and Lion el'Johnson become the ultimate brothers in arms each perfectly complimenting the other. In the canon this represented the bond between the Emperor's Children and Iron Hands
- The Dark Angels prove their loyalty to the Imperium and its ideals are beyond question. This is the equivalent of when the Iron Hands were tempted by the Emperor's Children to join Horus.
-The Thousand Sons fall out of imperial favour. There are several events that represent certain Legions being the least popular or left with unsavoury missions in canon such as the Night Lords and Iron Warriors.
-Night Haunter and Mortarion become the greatest (and most terrible) of comrades in arms.
-The White Scars butcher the people of their homeworld after they rebel. In canon this was the Iron Warriors attack on their homeworld of Olympia.