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) or 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 orkkind 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 reactions of the High Lords of Terra varied from total incompetence to outright hinderance of 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), costing more worlds and billions if not trillions of lives. There was one (later two) exception: 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 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 The Beast sent his diplomats asking for their surrender (yes, Ork diplomats were 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:

• Abdulias Anwar, Master of the Adeptus Astra Telepathica, was assassinated by a Culexus Assassin while praying for the Emperor to forgive his failures during the war. His soul was effectively obliterated by the Blank - a fate which his compatriot and politcal ally Volquan Sark, Master of the Astronomican, shared.
• Paternoval Envoy Helad Gibran was poisoned by his cousin Dovrian Ofar at the urging of Vangorich and the approval of the Paternova, who was displeased with the failures of his representative throughout the war. Ofar would subsequently replace Gibran on the High Lords as payment for the assassination.
• Juskina Tull, Speaker of the Chartist Captains and architect of the disastrous Proletarian Crusade, committed suicide via a las-pistol shot to the temple at the goading of her aide, Anastay (secretly an agent of Vangorich and possibly a Callidus Assassin), who told Tull of the millenia-long human tradition of becoming an hero after severely dishonouring oneself.
• Lord Commander Militant Abel Verreault and Lord High Admiral of the Imperial Navy Lansung were assassinated by a Callidus Assassin in the guise of Master of the Administratum Tobris Ekharth, who posthumously framed the two of them as having murdered one another during a dispute. Ekharth himself was likely disposed of earlier by the Callidus that assumed his identity.
• Grand Provost Marshal Vernor Zeck was killed by the Venenum Asssassin Beast Krule (keep that name in mind), who ambushed him outside of an Adeptus Arbites precinct deep within Terra's underhives. Unlike the rest of the High Lords, Zeck actually gave Krule pause in both words and combat for a minute before being killed and his head taken to Vangorich as proof of the kill, which would have significant consequences further down the line.
• Fabricator-General Kubik was forced to take shelter in his palace when attacked by an Eversor, only to be confronted by Vangorich himself, who threatened to unleash a powerful computer virus into the noosphere and essentially re-enact the Death of Innocence on the whole Martian database if Kubik did not voluntarily shut himself down. Kubik seemingly agreed, and handed over his intelligence core; in truth, Kubik had uploaded a copy of his consciousness to a hidden computer bank (or crafted an A.I. capable of mimicking his consciousness) beforehand to escape his inevitable death, only for Vangorich to promptly destroy this version of Kubik as well.
• Co-Inquisitorial Representative Veritus was poisoned by Vangorich several days before the coup, having unwittingly breathed in a gas that became lethal when combined with the chemicals of his life-support system. Although Vangorich initially intended to strong-arm Veritus into working with him via an antidote to the poison, this was later discarded after he committed to the coup. Veritus managed to warn his co-represenative to work with Vangorich, and try to prevent civil war by setting up the Ordo Hereticus; that done, he granted her the keys to access Titan and revealed his true identity as Kyril Sindermann, before finally passing away.

Vangorich himself was left top dog of the High Lords and had much of the council replaced with impostors and puppets (barring Inquisitoral Co-represenatative Wienand, Captain-General Beyreuth, and the psychic adeptae, with the last losing their places entirely), effectively making him sole ruler of the Imperium which he led for about one hundred years.

Vangorich's intentions were good and at first even the few who'd realized what he'd done were okay with it, as the War of the Beast had left the Imperium in shambles and a strong leadership was exactly what was needed. Initially, the Imperium thrived and remained strong and united under his rule, recovering well enough to sustain the Fourth Founding and restoring planets that had been ravaged by the Orks. Vangorich paid attention to rebuilding the Imperium's armed forces and was one of the biggest behind-the-scenes sponsors of the Deathwatch in order to ensure no xenos' threat could ever threaten mankind that direly again.

Sadly enough, no good deed remains unpunished in the 40k universe. As time went on, Vangorich's rightful concerns about xenos threats and the Imperium backsliding back into the state it had been while the Beast invaded turned into fear; fear turned to paranoia and paranoia eventually turned into complete lunacy. His reign was marked with massacres, vicious reprisal, harsh punishment, and increasingly totalitarian control, enough to make even the Inquisition nervous. Near the end of his reign Vangorich's paranoia and the stress of keeping the Imperium together eventually drove him to the point that he was giving insane orders such as randomly ordering mass planetary purges, assassinations, and massacres with no real reason and bankrupting entire sub-sectors to build increasingly grandiose monuments and vanities. In addition his increasingly erratic behaviour was finally starting to threaten the very stability that he had strived so hard to achieve, with even Eldrad forseeing that Vangorich's continued rule would lead the Imperium to eventual decay and destruction with no Roboute 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.

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, Thane really should have stayed behind to help get things in order instead of crusading). 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: Thane, 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 Thane if he would like to know how Konrad Curze died (possibly drawing a parallel between their intended roles in the Imperium) but Thane had none of it, killing him before he could answer. Only the 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, ironically as Vangorich had predicted. For a century 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 to cock-slap 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 recreate the actual Dark Age of Technology ability to teleport planets out of danger or fortress worlds right to the enemy. In a less amusing but unsurprisingly stupid move, this technology was never used to do exactly that at the time 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 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... in 926.M41. 9380 years later. It is possible that were refounded after their destruction (like with the Minotaurs), but this is not being hinted in what is known about them like with the Minotaurs. Offical canon lists 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. 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.