In the wake of the Horus Heresy, the Imperium was a dismal, shattered thing. As the beauty and grandeur of the Imperial Palace had been burned black in the flames of betrayal, so great swathes of the Emperor's star-spanning realm had suffered a similar fate. The Master of Mankind was a broken husk, and his dream of unity erased forever. Yet for all this, the Imperium retained might enough to exact a bloody revenge upon its foes. There could be no forgiveness for the crimes of the Traitor Legions -- those who now ruled in the Emperor's name had neither the ability nor the desire to prevent a war of reciprocity. So began the time known in the histories of the Imperium as the Great Scouring. Before actually being confined for all time within the life-support mechanisms of the Golden Throne, the Emperor had pronounced judgment on the Traitors: he declared them Excommunicate Traitoris, and determined that they were to be driven into the hellish region of the Warp rift called the Eye of Terror, which would hold them for all eternity. All records and memory of the Traitor Legions were to be expunged from the Imperial archives. Worlds such as Istvaan V and Davin would be scoured clean of all life because of their corruption by Chaos. The Traitor Legions' associated troops from the Dark Mechanicus, the Titan Legions or the regiments and starships of the Imperial Army that had turned to Chaos were to be destroyed or also driven into the Eye of Terror. It would be as if the Traitor Legions had never existed to sully the Imperium with their betrayal.
This was a period of monumental violence, of confusion and darkness. Though the newly founded Imperium fought to root out corruption and expose wrong-doers to the cold light of Imperial justice, the galaxy's scope and dark, shadowed reaches worked against them. With new betrayals and cries for vengeance emerging daily, a great many bloody-handed deeds went unseen. The ravaged Space Marine Legions were no exception to this, with many striving to cover up their own misdemeanours or exact their pound of flesh from those who wronged them. The Dark Angels, the Space Wolves, Iron Hands and even the Ultramarines, all followed their own agendas as the wars of the Great Scouring gathered pace. Fighting continued for another seven standard years after the Heresy had ended with Horus' death on the bridge of his great flagship, the Vengeful Spirit, before the Traitor forces were wholly destroyed or exiled into the Eye of Terror. Many Chaos-corrupted star systems were cleansed and placed under the watch of the newborn Inquisition. Horus' death had not ended the fighting, but it had renewed the resolve of the Loyalists to destroy the Traitors. Many Imperial worlds during the Heresy had refused to commit their forces to either side, or seceded entirely from the Imperium to regain their independence. Such indecision was punished by Loyalist and Traitor forces alike. These forces were often bled white attacking the rebel strongholds of worlds that only wanted to be free of the Imperium entirely, whether it swore allegiance to the Emperor or to the Dark Gods.
Changes swept both the Imperial military and the offices of government. The Space Marine Legions, the vast fighting formations so instrumental in Mankind's victories during the Great Crusade, were broken down into many smaller Chapters comprised of 1,000 Astartes. Overseen by Roboute Guilliman, the Primarch of the Ultramarines Legion, he penned his magnum opus, the Codex Astartes -- a great and sacred tome which covered every conceivable topic of military organisation, strategy and tactics. This transition allowed for greater tactical flexibility without placing the command of an entire Space Marine Legion into the hands of one individual -- never again would the awesome power of one hundred thousand Space Marines be misused. The Loyalist Space Marine Legions that had been decimated during the Drop Site Massacre on Istvaan V -- the Raven Guard, Iron Hands and Salamanders -- were slowly reestablished using what little gene-seed the survivors had managed to escape with. The original First Founding Space Marine Legions were divided into smaller Successor Chapters -- one Chapter maintained their parent Legion's original name, badge and colours, while the remaining Chapters took new names and heraldry. These original Chapters are known as the Second Founding Chapters, an event which occurred in the early 31st Millennium and coincided with the beginning of what was known as the Reformation of the Imperium.
Another vast change wrought upon the Imperium's mighty military redefined the nature of the Imperial Army. Once including both the great battleships that plied the stars and the countless soldiers that landed to fight planetside, now the two were divided into the Imperial Navy and Imperial Guard. Across all the agencies of the Imperium, offices and institutions were split, their previous responsibilities fractionalised into separate functions and departments. Many of the countless branches within the sprawling Adeptus Administratum were spawned at this time. With the instigation of these changes, it was not unusual for two separate organisations, each unaware of the other, to be tasked with the same jobs, such as verificator scribes and tithe enumerators poring over the same data, each producing the same reports. These byzantine systems were put in place as fail-safe measures, which have since spiralled out of control into administrative excess. Beyond any such bureaucracies, and standing watch over all, was the newly formed Inquisition, a secretive paramilitary police organisation outside the established hierarchies. Ever vigilant, their role was to question everything in their constant search for threats to humanity. None save the Emperor Himself escape their uncompromising and watchful gaze.