Shattered Imperium

Loyalists

Some of the Legions have stayed loyal to the Emperor and His vision of a Secular Imperium, Entering a Golden Age.

Imperial Fists

Raven Guard

Salamanders

Blood Angels

Traitors

As in the main 40k setting, Lorgar discovers the powers of Chaos and attempts to lead his brother's into their all-too-eager arms.

Sons of Horus

Word Bearers

Alpha Legion

White Scars

Path Of Ascension

The Forces of the Path of Ascension, sometimes referred to Ascensionists, are a transhumanist movement who believe that humans need to evolve to survive the perils of the Galaxy. Their methods vary from cybernetic enhancement to trying to turn all humans into Psykers

Thousand Sons

Iron Hands

Emperor's Children

Free Legions

The Free Legions are a revolutionary force in favour of overthrowing the Tyranny of the Emperor and replacing it with a more egalitarian government. At the same time, they feel that Horus and his forces are corrupt and as likely to damn the human race as the Emperor or Path to Ascension.

Death Guard

Iron Warriors

World Eaters

Night Lords

Renegades

Ultramarines

Guilleman, still technically loyal to the Emperor, has hidden himself way from the rest of the galaxy and created his own semi-autonomous Imperium Secundus

Dark Angels

Lion El Johnson left the imperium decades ago after the indignation of not being chosen as warmaster. He feels that if he can't be the heir-apparent to the Imperium, he might as well just make his own empire.

Space Wolves

Russ hates Magnus the Red more than words can describe. He has abandoned any semblance of loyalty or duty in his own personal crusade to crush Magnus and his sons.

The Purge of the unknown Legions.

Early in the Great Crusade, the 2nd and 11th legion stray from the Emperor's light and in turn he smites the legions with the aide of Russ, his executioner. Whilst several of the Primarchs feel that this action was necessary. Guilleman speaks out against it and is reprimanded by Horus and Dorn who feel he is overstepping his mark. Less publicly, Perturabo and Mortarion equivocate the Emperor to the tyrants of their own adoptive homeworlds.

Lorgar's shame

The Emperor, fearing that 2 more of his sons have drifted from his will, devises a plan to test the loyalty of the 13th and 17th legions. Guilleman is ordered to destroy the city of Monarchia, the crowning glory of Lorgar's zealous crusade. Guilleman resists but eventually obeys when he realises that the Emperor is willing to set Russ on him if he doesn't. Lorgar and Guilleman come to blows after the incident and both of them lose their faith in the Imperium. Across the Legions, there is talk of whether or not the Emperor's judgment is impared somehow. Soon, Guilleman is back in Ultramar and Lorgar is facing the Primordial truth.

The Alpharius Gambit

An Eldar/xenos cabal approaches the twin primarchs with a warning of the impending fall of Horus and the fracture of the Imperium. Their emissary implores the 20th Primarchs to slay Horus and Help the Emperor purge the Ranks of the Astartes legions. The twin Primarchs slay the foul xenos and set off to find Horus at once. Along the way, they examine evidence of the Primordial annihilator, seeking to understand this bizarre force so they can harness it.

The Nikaea Schism

After years of open hostility between Magnus, Mortarion, the Khan and Russ, the Emperor calls a trial to discuss the use of Psykers within the Legions. Mortarion makes an impassioned speech about the dangers of the Librarian cult and the troubling rituals that the Khan and Magnus have engaged in. Magnus responds with his own beleif that humanity must be ascended to survive some unkown horror that he perceives in the future. The Khan and Russ trade insults for a while before the Emperor makes his judgment known. The Librarian cults will be permitted to continue and will be implimented within all legions, to hasten the ascension of the Legions. Mortarion leaves the conclave, completely disillusioned with the Imperium. He seeks out his like minded brothers to discuss a response to this betrayal. Meanwhile Magnus, overjoyed by the Emperor's wisdom, commits his legion to the Crusade with new vigour.

The Fault in the Stars

On Davin, Horus is seduced to Chaos by his brother Lorgar. Magnus is never made aware of the peril his brother faces as he is away from Prospero. The Alpha Legion arrive soon thereafter, already twisted to the Malign will of Tzeentch by their quest to understand Chaos. Together, 4 Primarchs plot Heresy.

Magnus joins Ferrus Manus and Fulgrim in a joint crusade to crush an Eldar Craftworld. While there, Magnus discovers that Fulgrim has been tainted by the malign influence of a daemon-blade. He informs Manus and together they help stop the insidious creep of Chaotic influence over the 3rd legion. Magnus explains what has happened to his deeply concerned brothers and explains how he has saved Fulgrim from possession. Fulgrim devotes himself to Magnus' cause. Ferrus Manus takes more convincing but ultimately agrees that psykers are more powerful and so must be made superior. Together, they plot a new future.

Mortarion meets with Perturabo and Angron. The Iron Warrior is attempting to rid the Red Angel of his Butcher's nails using a bizarre new invention of his. Mortarion and Perturabo are overjoyed by the apparent success of the procedure, but it isn't long before Mortarion begins discussing the results of the Nikaea conference. Perturabo is dumbfounded by this revelation. Together, the 3 Primarchs agree that they must save Humanity from the madness of Magnus the Red and the Emperor. But first, Perturabo wishes to Seek out the mad primarch, curze, and cure his insanity

In the deep, Russ and Lion El Johnson battle over past wrongs and minor slights. Both of them are driven by a sense of betrayal. the Lion is furious that Horus Lupercal, not he, was made Warmaster. The Wolf refuses to allow Maleficarum to take hold of his legion. Both Legions throw off the shackles of imperial law to impose their own.

Jaghatai Khan strives for perfection and speed. His White Scars engage in shamanistic ritual sacrifice and indulgence in order to gain the blessings of the various spirits. When Horus calls onhis brother to join him, the Khan is already well and truly damned.

The Isstvan War

Magnus is summoned to Isstvan by his brother Mortarion. The Death Lord wishes to mend old wounds and hear more of Magnus' plans. Happy to hear that his brother has seen the light, Magnus sets out, with his two likeminded brothers, to bring the Death Guard into the fold.

When they arrive, the Ascenionist fleet finds not 1, but 3 legions arrayed before them. The Death Guard, Iron Warriors and World Eater fleets wait patiently over Isstvan 3. Mortarion greets the Acenionists and invites them to the capital city of Isstvan 3, to meet with their brother. Weary, but ambitious, Magnus accepts and leads his 3 legions to the surface.

He talks with Mortarion at length about the threat of Chaos and the the neccessity of knowledge. Perturabo seems the most receptive to Magnus's arguments and they discuss, at length the ascenionist plan. Suddenly, without warning, Mortarion's forces open fire on the Ascencionists. Magnus barely escapes the clutches of Perturabo. His own son, Ahriman sacrifices himself for the Thousand Sons to escape the planet.

Battered and shocked, Magnus leads the Ascenionist fleet away from Isstvan 3 at best possible speed. As they reach Systems edge, an astropathic message is recieved. Prospero has been destroyed by the Space Wolves. Chemos and Medusa have been purged by the Night Lords.

Blinded by rage and grief, Ferrus Manus and Fulgrim turn their forces back toward their would be assassins. Magnus has no choice but to join his brothers or see them destroyed. What follows is a chaotic, violent maelstrom of void combat and planetary bombardment.

When word reaches the rest of the Imperium that 6 legions have turned on one another in the Isstvan system, the warmaster declares all of them traitors and rallies a force to cleanse them. The Sons of Horus, the Word Bearers, the Alpha Legion, The White Scars, The Raven Guard, The Salamanders and the Blood Angels. 7 legions to destroy 6.

The Warmaster's fleet arrives to find both enemy fleets scattered, Isstvan 3 a lifeless husk and a brutal ground war underway on the barren world of isstvan 5. Horus orders Sanguninius to lead Corax and Vulkan to the ground on Isstvan 5 immediately. The Blood Angel gladly complies and deploys 3 assault legions to strike for the heart of the melee, where Magnus and Mortarion are locked in duel.

9 legions, Locked in a battle of cyclopean scale, await the second wave of loyalists. Instead, they are all of them betrayed. Horus Begins an orbital bombardment of the battlefield, slaying Ascenionists, Loyalists and Free Legion forces alike. The Warmaster makes a pronouncement. They may join him in his new dark crusade to claim Terra, or they may die in the sand. All 9 Engaged Primarchs spite the name of Horus. Amused but unsurprised, Horus prepares t destroy Isstvan 5.

On the Ground, a truce is formed. The 9 legions, battered and bloodied forstall their current conflict in the name of survival. The Ships of all 9 legions focus their attentions on the Warmasters fleet in the hopes of gaining enough time to evacuate the armies on the ground.

The Fighting is intense, and Horus is forced to surrender his position above Isstvan 5 to the overwhelming firepower of his foes.The Free Legions, Aided by the sudden appearance of the Nightlords, inflict heavy casualties on the Traitors before fleeing the system.

Sanguinius and the Loyalists save the remaining acensionists, what few are left. and flee towards Terra. Magnus repays the mercy of the Blood angels by stealing several of their ships to carry his remaining followers towards some unknown goal on the edge of the Imperium.

Horus rallies his armies and declares a victory for Chaos and prepares to set his brother's to the task of carving up the Imperium.

The Civil War.

The Warmaster strikes across the Imperium, claiming world after world for chaos. His ultimate goal is to take Terra and become the Emperor.

Battered and severely diminished, the loyalists turn to the Imperial Fists to lead the defence of Terra and the Counter Attack to reclaim the Imperium.

Robute Guilleman, at a loss as the the sheer scale of this betrayal, fortifies the worlds of Ultramar into a second Imperium. There are rumours that the Dark Angels, dissapeared for decades, have been sighted near Ultramar, making their way towards the system of Calth.

Magnus, witha meagre host of survivors, makes his way towards a strange, dead world world near the edge of the Galaxy, where it is rumoured that a powerful psychic device is hidden. Magnus wishes to restore his forces to strength and save humanity. All the while, wolves nip at their heels.

Mortarion and the Free Legions move out of the way of the War, claiming large areas of the Imperium that were cut off from Terra as their own. He and His brothers set about remaking the imperium in their own image, all the while gathering allies and strength so that they can put an end to the madness of Horus and the Emperor

Xenos collaboration

Loyalists are slightly more open to xenos than the original imperium primarily because they only had a few legions and lacked the numbers to truly defend their space without some negotiation with xenos. Main allies are craftworld Eldar but as with the Imperium secundus conflict does erupt from time to time.

Chaos are pretty much chaos from our timeline with the exception that Dark Eldar never interact with them as they are full Chaos and have no real renegades (Like Fabius Bile or the Night Lords) who just use chaos for their own means.

Free legions see xenos as a stepping stone for their objectives generally. While they will not hesitate to exterminate races that are enslaving humans they will gladly ally with minor xenos races if it means gaining an advantage.

The Path of Ascension is more than willing to utilize xenos knowledge and technology but tend to view xenos allies as a weakness that will lead to the collapse of the path. So some haemonculi might be tolerated to modify marines and the Iron Hands descendants might study Necron tech but you won't generally see PoA fighting alongside Necrons or Eldar.

Renegades vary. Space Wolves probably kill them all, Lion doesn't care as long as they kneel before him, Guilliman is more willing to utilize xenos as auxiliaries for his armies.

Aftermath

So what would be the overall fates of the major characters? My thoughts.

Dorn, Sanguinius, Corax, and Vulkan are all either dead or missing. The Emperor is left crippled on the golden throne or he finished the webway project but is completely dead.

Horus is dead as can be, Alpharius is somewhere maybe, Lorgar is praying, and Khan is a daemon prince launching massive wars against the Imperium every thousand years or so.

The Free Legion primarchs are all still alive and doing their own thing as the Imperium couldn't devote forces to them until Chaos was defeated.

Magnus is studying and meditating to become a more powerful psyker as well as hording artifacts that improve psychic capabilities in the hopes of ascending as a psychic god. Ferrus is like Scoria on steroids, having begun to mechanically augment himself and studying dark technology to improve humanity through cybernetics, he may have found some working men of iron who he intends to fix and release onto the PoA. Fulgrim is the de facto ruler and administrator of the path, while still seeking perfection in all forms and while he still sometimes leads armies to battle he primarily deals with running the path, organizing their armies, and carrying out ceremonial duties.

Lion is alive and ruling his empire

Guilliman has left running of his empire to a senate made up of planetary governors, he is Lord Commander of the Imperium Secondus, commander of all armies and fleets and an observer on the senate. Most recently he led a force of tens of thousands of marines, tens of millions of regular human soldiers, and hundreds of thousands of various xenos auxiliaries against the Tyranids

Leman Russ has gone missing after pursuing Alpha Legion near the Eye of Terror. He is currently presumed deceased by all except the Wolves who continue their war without their father.

I like that, yeah. I feel like Each of the Free Legion Primarchs have probably drifted slightly from their original Imperative.

Mortarion rules the Free realm as eternal protector. His sons, Under Nathanial Garro keep the realm untainted by chaos. They use a network of inquisitive people to keep their realm pure.

Perturabo has devoted himself to building technological wonders for the Realm and to maintaining the technological superiority of th Free Legions.

Angron has abandoned any official role within the Free Realm and instead leads crusading armies to liberate systems from the opression of their brother-states.

Curze is the Justicar of the Free Realm. He polices the Interior and keeps his legion on the prowl for any source of treachery.