The Beheading

The Beheading was an event in 546.M32 where Drakan Vangorich, the Grand Master of the Officio Assassinorum rebelled against the High Lords of Terra. He might have actually been the good guy (in the sense of not murdering people who don't cause problems and murdering people who cause problems for Imperial citizens). He might have been the bad guy (from the perspective of "the punishment must match the crime").

Coup

In the mid-32nd millennium a great calamity befell the Imperium: the WAAAGH! Beast. The most vicious rampage made EVER by orkind drove the Imperium to its knees as dozens of Space Marine chapters were annihilated, the Imperial Fists were reduced to a single Astartes, and thousands of worlds were put to the torch. Terra itself was in a state of constant threat during a good chunk of the war.

The reaction from the High Lords of Terra varied from total incompetence to outright hindering the war effort (special note goes to the Ecclesiarch who wanted to WORSHIP the Orks and abandon the cult of the Emperor, and the Fabricator-General who just wanted to loot the Orks' tellyporta technology so the AdMech could teleport Mars out of the way, leaving Terra to its fate (extra stupid points to him since the only reason Mars was in danger was his demand that the Imperial Fists not destroy the Attack Moon so he could get the teleporter technology from it) and thus costing more worlds and billions if not trillions of lives. Except for one (later two): Drakan Vangorich, the Grand Master of Assassins himself; and in spite (or perhaps because) of such a grim task, he was a bona fide patriot. He and de facto Chapter Master Slaughter Koorland made great efforts and maneuvers to get the filthy and complacent asses of the High Lords to work on the threat at hand. It suffices to say the two of them may be amongst the greatest heroes of the Imperium, for without them mankind would have been annihilated or reduced to savagery a la the Age of Strife.

Once the war was over, Drakan realized that, should there be another threat of a similar calibre, mankind would be wiped out due to the incompetence of the High Lords. This was especially evident when, as The Beast sent his diplomats asking for their surrender (yes, Ork diplomats had become a thing, thanks to the Beast), the High Lords were more concerned about their own political power than saving mankind. The final straw came when Vangorich found out that the Fabricator-General had teleported Ullanor away instead of Exterminatus-ing it as ordered; the planet eventually became Armageddon. For the sake of the Imperium, the High Lords needed to die, and die they did. With the resources of the Assassin's temples at his call, it wasn't too hard for Vangorich to kill / replace every other member of the High Lords within five days. Vangorich himself was left top dog of the High Lords and had the rest of the council replaced with impostors or puppets making him sole ruler of the Imperium, which he led for about one-hundred years.

Vangorich's intentions were good, but he grew increasingly paranoid about the Imperium ever backsliding back into the state it had been before the Beast invaded. So while on the good side he did rebuild the Imperium's armed forces and restored planets that had been ravaged by the Orks, his reign was marked with massacres, vicious reprisal, harsh punishment, and increasingly totalitarian control. And for those wondering these were far more than usual, that even the inquisition was nervous. The Imperium remained strong and united under his rule (recovering well enough to sustain the Fourth Founding). But things didn't stay good forever. Nearing the end of his reign Vangorichs paranoia and the stress of keeping the Imperium together eventually drove him insane. With Vangorichs mental state deteriorating to the point that he was giving insane orders such as randomly ordering mass plantery purges, assassination's and massacres with no real reason and bankrupting entire subsectors to build increasingly grandiose monuments and vanities (though in a slight bit of his old self remaining, statues of Koorland were usually the largest). In addition, his increasingly erratic behavior was finally starting to crumble the very stability that he had strived so hard to achieve (with even Eldrad forseeing Vangorichs continued rule would lead the imperium to eventual decay and destruction. And there would be no Robuoute Guilliman to fix things). Terra finally grew sick of living in constant fear of their single ruler and eventually a coup was formed.

The Astartes and Inquisition, agreeing on a unified goal for a change, decided that it was time to relieve Drakan Vangorich from office. Every other department in the Imperium (barring the Assssinorum, of course) stepped aside to let them do it (granted, no other departments have military strength except the Administratum and the Inquisition could just flash their rosettes in that case).

Response

A strike force of 400 marines led by the Imperial Fists under Chapter Master Maximus Thane and supported by elements of newly created chapters (The Halo Brethren and Sable Swords specifically) landed on the Imperial palace to hunt down Drakan and seize control of the Senatorum Imperialis. The Officio responded in kind, deploying its most lethal operatives: the landing zones became killzones filled with snipers and the disembarking Astartes were assailed by hundreds of assassins from various temples. Callidus and Culexus harassed their advance, while Vindicares took shots at them from every angle. Venenum and Vanus operatives probably worked from behind the scenes to hinder their advance, but strangely no Eversor assassins were present. Despite losing half their numbers in the process, the Astartes managed to carve their way through the assassins and clear out the Senatorum for the most part. Thane then confronted Inquisitorial Representative Wienend, who revealed Vangorich had fled to the Eversor temple at the North pole. Both had a row of words lamenting the situation before Thane departed to hunt Vangorich down. Wienand stayed behind to die by a bomb trap Vangorich had placed in the Senatorum (she was aware of it, but felt it appropriate to go out with a bang given the circumstances).

The remains of the strike force assaulted the temple and confronted Vangorich, who had some final words with Thane, with both accusing the other of having some responsibility for the current situation (to be fair, running the Imperium would eventually drive anyone crazy, and Thane really should have stayed behind to help get things in order instead of crusading). Regardless, Vangorich sprung his trap by flooding the room with smoke and unleashing one hundred Eversors on the Astartes. The two forces cut each other down till only three remained: Chapter Master Thane of the Imperial Fists, Vangorich, and a single Eversor (Beast Krule, a former favored assassin of Vangorich who had been forcibly converted into an Eversor after betraying Vangorich earlier). Vangorich ordered Krule to cut down Thane, but the Assassin broke his programming long enough to refuse, giving Thane time to get a bead on Vangorich. Oddly, Vangorich's last words were asking if Thane would like to know how Konrad Curze died (possibly drawing a parallel between their intended roles in the Imperium) but Thane was having none of it, killing him before he could answer. Only a badly-wounded Thane survived the ordeal and Vangorich was left to go down in history as a cruel tyrant.

Over the next millenia, many reformations were implemented to prevent one person gaining complete control of the Imperium and causing such trouble (abolishing the position of Lord commander of the Imperium, for instance), helped along by a certain asshole being another great example of what the Imperium does NOT need in a leader. Also, the Ordo Sicarius was set up to keep some assassins pointed at the assassins.

Aftermath

In the immediate aftermath of Vangorich's death the Imperium fell into a state of anarchy, as everyone and their sisters vied for a place in the new version of the Senatorium Imperialis, leading (ironically as Vangorich had predicted) to yet another period of anarchy due to human incompetence. For a century long there was no central leadership and no official successors for the High Lords as people vied and struggled for political power. Luckily Agnathio, the then-Chapter Master of the Ultramarines got fed up with this shit real quick, gathered up no less than fifty of his fellow Chapter Masters and their Space Marines; and they all set course for Terra where they proceeded with cock-slapping everyone in the Senatorum until once again twelve High Lords were chosen, finally restoring stability to the Imperium.

In an amusing twist, the Imperium studied scientific-ish Ork tech to re-create the actual Dark Age of Technology ability to teleport planets (DAoT could teleport star systems, though) out of danger or fortress worlds right to the enemy. In a less amusing but unsurprisingly stupid move, this technology was not used to do exactly that ever or in the future and was not used for ship interstellar travel, either.

Clash of the Canon

One of the Chapters who fought against the Assassins was the Sable Swords. The Chapter that is currently known as the Sable Swords was formed to replace the remnants of the Astral Knights, nearly wiped out during their siege of The World Engine… which was in 926.M41. 9380 years later. It is possible that they have been refounded after their destruction (like with the Minotaurs), but this is not being hinted in what is known about them like with the Minotaurs. Or it could have been another fuckup, who knows.

The Offical Canon does however list the Sable Swords as Losing over 800 Marines in the fighting. So they were most likely Massacred and re-built.

In addition, there's a footnote in the fluff that says the administratum didn't realise that there were two chapters named the Sable Swords until both were destroyed in fighting in the 13th Black Crusade. This probably explains it.

The Imperium is really big, the only way to communicate is via psychic mind pictures and the only way to travel occasionally hurls you through time, and Chapters are almost always split up across multiple warzones. With that in mind, it's somewhat miraculous that this is as mixed up as things get.

Although, given there's only around a thousand loyalist Chapters and they're kinda just a teeeensy bit important, you'd think even the Administratum would do its utmost to keep track of every little thing related to the Adeptus Astartes. Especially after a certain infamous temper tantrum.