Indomitus Crusade

"To the Space Marine Chapters bloodied and besieged in the Dark Imperium, we bring reinforcement. To the Chapters lost in valiant duty or driven to destruction, we offer rebirth. To the enemies of my father's empire, we bring death. With these words I, Roboute Guilliman, Lord Commander of the Imperium, son of the Emperor of Mankind declare the Indomitus Crusade. Traitors, mutants, daemons. Heed to the coming of my armies and the ruin we promise to your miserable kind. This galaxy is ours!"

– Roboute Guilliman, Lord Commander of the Imperium, son of the Emperor of Mankind.

Roboute Guilliman, trying to channel as much the Emperor's charisma as possible while the sky goes bananas on him

The Indomitus Crusade is the Imperium's latest major military campaign, in response to Abaddon's 13th Black Crusade, its successful destruction of Cadia and the fracturing of the galaxy in two pieces. After the combined efforts of Archmagos Cawl, Saint Celestine and the Ynnari to bring the Primarch Roboute Guilliman back from stasis, he reaches Terra and takes full control of the Imperium to try and get shit done. To do this, he declares a massive crusade to push back the forces of Chaos, unveiling his brand new and very marketable Primaris Marines to spearhead his attack against Chaos, even if no one really trusts these new guys. The Indomitus Crusade lasted around a century and managed to stabilize the Imperium, but the 13th Black Crusade is technically still going on. Also, this event is the first major step into the 42nd Millennium (or not because calendars are fucked in this grimdark future), Ciaphas Cain's novels notwithstanding.

This event is especially remarkable because this is the biggest advance of the 40K storyline in decades, making people really afraid of this being another Age of Sigmar. For now, those fears have been pushed aside; the galaxy is still there, although split by the Cicatrix Maledictum.

Phase 1: Gathering forces and the Second Battle of Terra

Soon after Guilliman arrived to Terra and took the title of Lord Commander of the Imperium (basically becoming the de facto ruler of the Imperium of Mankind and Head of the High Lords of Terra), he started to gather up all the forces he could to counter the forces of Chaos that were pouring from the Warp in massive amounts: Astartes, Mechanicum, Navy, Guard Regiments, the Sisters of Silence, some Custodes elements (finally entering the galactic fray after millennia of doing fuck all), and the new and now on sale Primaris Marines to spearhead the counterattack. While he was busy gathering his forces Terra was attacked by the Legions of Khorne. The Blood God was fed up with the other idiots mucking about around the Cicatrix Maledictum believing they'd won, so he went to finish the job on his own and sent in eight of his Legions... who were quickly and swiftly sent running back to the Warp with extreme prejudice and overwhelming firepower.

This small incursion, however, caused massive panic and unrest on Terra proper. The Terran anti-Warp defenses failing to prevent the opening of a rift from where Chaos attacks could pour from was a major concern, and some argued that Guilliman should stay to defend Terra. But the Primarch knew that to prevent the situation from going completely bad he had to bring the fight to the enemy. His forces set out from the centre of the Imperium, course set for the hundreds of planets either under siege or already conquered by the Ruinous Powers. During all of this, the Astronomicon was not working properly, constantly flickering and making Warp jumps a pretty risky move. And considering Guilliman's Crusade used almost half of the Navy Fleet in Segmentum Solar, they had to do very short jumps, slowing the beginning of the Crusade down considerably.

Phase 2: Guilliman frees a bunch of planets and brings Primarines to the Chapters

Guilliman soon arrived into the thick of things. He travelled around dozens of planets, liberating those that could be saved and exterminatusing those that could not. Slowly but surely, Imperial forces managed to push back the chaotic tide. Albeit only enough to stabilize some of the war fronts. The arrival to Catachan was a specially interesting point in the Crusade: the planet's local fauna was so deadly it scared away even the daemons, which probably brought a decent amount of morale-uplifting laughter to the Imperial forces involved. As the tides of the Warp calmed, astropathic communications started to improve all around (even if the Imperium Nihilus was still pretty much isolated from the light of the Astronomican). The more planets the Primarch freed, the more reinforcements he added to his campaign and the more momentum it built up. During this phase of the Crusade they went to the other side of the Imperium, the part that would be known as the Imperium Nihilus or Dark Imperium, and saw the horrible things that had been going on there without a consistent shine of the Astronomican. They came across the massive meatgrinder that was the Battle for Baal between Hive Fleet Leviathan and all the Blood Angels' descendant chapters Dante could muster. Even though the battle was pretty much over when Guilliman arrived (stated by himself to Dante once the fight was over), Guilliman used his enormous fleet to purge and chase away as many splinter fleets of Leviathan as possible before the reconstruction of Baal and before they could restart the crusade against Chaos. Guilliman also appointed Dante as the military leader of the Imperium Nihilus, which means he has the maximum authority over half of the Imperium, only below the Primarch and the Emperor.

It is also during this phase that the already extant Astartes Chapters started getting their Primaris reinforcements, with all manner of colourful reactions. After much grumbling, the general consensus ended up being "accept them or the Adeptus Custodes will shove a Guardian Spear up your ass, also fucking hell we need the manpower".

Phase 3: Nurgle attacks Ultramar and Guilliman ends the Crusade

After a century of war and freeing planets beyond count, the front was largely stabilized, Chaos contained into the Cicatrix Maledictum, and tentative contact had been reestablished with Imperium Nihilus. Guilliman's forces were however exhausted and Belisarius Cawl needed to refill the Primarines' ranks. Many of the crusading forces wanted to consolidate their gains rather than continuing the conquests and stretching their forces thinner and thinner throughout the galaxy.

The deciding point was the invasion of the Ultramar realm by the forces of Nurgle, taking advantage of the drawing of forces for the Crusade leaving planets relatively undefended. Thus after the Battle of Raukos on 111.M42, Guilliman called it a day and dissolved the Indomitus Crusade, capping off the Ultima Founding by disbanding the final core of Unnumbered Sons veterans to new Primaris chapters, allowing everyone to go home and deal with the invasion. With that, the Indomitus Crusade reached its end on a globally positive note as the 13th Black Crusade had been mostly contained and the situation was no longer deteriorating quite as badly as it was before, which is probably the closest thing to a change for the better within the setting since, well, ever.

The Retconning

So 9th Edition decided for whatever reason to retcon the crusade from concluded to still ongoing, with the Raukos conflict merely wrapping up a phase in the larger crusade. Probably because there was no reason to end the Crusade. You cannot win a war just by defending. To say nothing of how the Imperium, Adeptus Astartes, and countless other major factions would view ending the most important and successful offensive since the freaking Great Crusade merely because a few planets in Ultramar were invaded. Because of this new corporate direction, the entire Dark Imperium series of novels is being rewritten to better fit the situation in the Dawn of Fire novels and everything else (including the recent Psychic Awakening series to an extent) being built around this.

Results of the conflict

The Indomitus Crusade managed to push the forces of Chaos long enough for the 13th Black Crusade to start losing its momentum (because Chaos doesn't stay organized for long and a lot of its warlords decided to start pillaging nearby systems rather than keep pushing towards Terra), thus preventing more damage from being done. This doesn't mean that the Imperium didn't suffer a massive blow: the Cicatrix Maledictum and the losing of planets in hundred thousands means this was the biggest blow the Imperium has suffered since the days of the Horus Heresy or the War of the Beast. And you can be sure those worlds in there are going to be shitting out Dark Mechanicum, Lost and the Damned, and Daemonic threats soon enough once they fully get their Chaos on. The only saving grace is that the process would devastate the worlds within and their populations and Chaos isn't all that good at building stuff compared to everyone else.

The Dark Imperium Stabilizes

Half of the Imperium still gets barely any light from the Astronomican, isolating the Imperium Nihilus from the Emperor's light and also cutting it off from any reinforcements that might come from the other side of the Imperium (except through one available warp route occupied by a traitor Knight House or, y'know, going around or above or under the Great Rift), exposing it to future attacks from heretics and xenos alike and making warp travel an even more hazardous experience. The splitting of the Imperium into two halves (one that is able to keep itself stable enough due to Guilliman and being on the same side as the Astronomican, and one which is basically daemon food) is bound to cause problems on the off chance there's enough of the Imperium left to break away in the Imperium Nihilus, not to mention that most Chaos forces are still running amok throughout the galaxy and now have a gigantic base of operations to launch their attacks from instead of the much smaller Eye of Terror and the Maelstrom.

That said, the Primaris reinforcements to the Dark Angels and Blood Angels have alleviated the worst of the 13th Black Crusade's rampage, so it's not entirely hopeless. Dante is also honored by Gulliman and placed in charge of the Imperium Nihilus when he can't get to it, so they're not without any sort of leadership.

Other Imperial issues

The Primaris Marines debate has only gotten worse after the end of the Crusade, with most people seeing Cawl's creations as either necessary abominations or an outright heresy, depending on whom you ask. If Guilliman speaks soon and intelligently, this could be dismissed by his pointing out the Primaris are made from the most pure gene-seed in a device created by the Emperor himself using techniques used in the creation of the Custodes, so calling it heresy is like saying the Primarchs and Astartes in general are heretical. The Custodes know the Emperor approves, and the Custodes do not like it when people refuse the Emperor's will.

On the administrative side, Guilliman has to manage several warzones at once while ruling the whole Imperium and dealing with the various groups that are opposed to his attempted reforms, which is a difficult task even for the Primarch known for his administrative skills. It'll be fine once he realizes that the current Imperium would be totally chill with him just exterminating all the groups opposing him. Even if he tried to wipe out the Ecclesiarchy the vast majority of people wouldn't see a heretic destroying worship of the Emperor but instead would see their religious institution refusing to roll over and die on the whim of one of the God-Emperor's own sons and are therefore heretical for not dying when their god's son told them to. The Mechanicus's higher echelons are also highly annoyed that Cawl is calling so many shots, and only Cawl's seniority and knowledge of many long-lost technologies has kept them from declaring him a heretek, which is funny because he was a key part in creating the Primarines and their armor so anything he does with it can’t really be considered heresy as the Emperor gave him leave to manipulate Astartes genetics to do his job in the first place before the Great Crusade. Of course, this assumes the Emperor = Omnissiah thing is still a thing. Considering the political/religious tensions Guilliman's caused in the Imperium Proper since his return... yes, it's still a thing, since Mars has not been blown up. The Mechanicus knows full well that to reject the Emperor as Omnissiah would mean extermination by an Imperium that genuinely would not give a damn what the consequences would be so long as they could purge heretics.

Xenos

Meanwhile, the Tyranids ate some more planets and are pushing further into Segmentum Solar, the Tau lost a whole expansion sphere when they ran straight into the Death Guard's main force, the Necrons expanded some of their empires, the Orks did what Orks do (hint: it involves Waaagh!, choppa and dakka) but they're more organized now, and the Craftworld Eldar are trying to figure out what to think of the Ynnari while generally attempting to not get wiped out by Chaos. The xenos and the danger they pose haven't gone anywhere, but for the time being the Imperium considers Chaos to be the more immediate threat to its existence.