The "Great Scouring," or simply "The Scouring," was the Imperium of Man's great counter-offensive against the Traitor Legions. It began immediately after the end of the Horus Heresy following the death of the Warmaster Horus and the failure of his assault upon the Imperial Palace during the Siege of Terra in 014.M31. Over the course of many solar decades, it finally succeeded in driving the forces of Chaos from their conquered territories within Imperial space into finding a refuge in the permanent Warp storm known as the Eye of Terror.
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 Eye of Terror for all eternity. All records and memory of the Traitor Legions were to be later expunged from the Imperial archives.
Worlds such as Isstvan V and the former Legion homeworlds of the Traitor Legions would be scoured clean of all life because of the corruption of their people by Chaos. The Traitor Legions' associated troops from the Dark Mechanicum, the Titan Legions, Chaos Knight houses or the regiments and starships of the Imperial Army and Imperial Navy that had turned to Chaos were to be destroyed or driven into the Eye. It would be as if the Traitor Legions and their allies had never existed to sully the Imperium with their betrayal.
After the death of Horus, those Traitors who had not been slain outright during the Siege of Terra fled before the vengeful wrath of the Loyalist forces led by Primarch Roboute Guilliman of the Ultramarines Legion, who also took on the burdens of leadership of the Imperium as the Imperial Regent and Lord Commander of the Imperium in the Emperor's absence. Many Traitors made good their escape into unexplored space or disappeared into the Eye of Terror or other, lesser-known Warp rifts such as the Maelstrom.
Fighting continued for many standard years after the Heresy had ended with Horus' death 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. The Emperor's dream of a new age of enlightenment, a time when Mankind was freed from superstition and ignorance, would turn into something far different. The Great Scouring would be followed by the ten-millennia-long era known as the Age of the Imperium.
In the midst of the campaigns of the Great Scouring, the Second Founding occurred. The remaining 9 Loyalist Space Marine Legions were disbanded, their transhuman warriors transferred into the far smaller 1,000-Astartes organisations known as Chapters, in accordance with the newly-established dictates of the Primarch Roboute Guilliman's Codex Astartes. The Codex provided a highly-detailed manual and instruction guide for the raising, training, organisation and military tactics of a Space Marine Chapter.
The purpose of this reorganisation was to prevent any one leader like Horus from ever again making use of the power of an entire Space Marine Legion against the Emperor's realm. At the same time, because of their smaller size, the Space Marines were transformed from the Imperium's primary frontline military forces into a dedicated planetary assault and rapid reaction force.
A portion of the Space Marines, now collectively known as the Adeptus Astartes, maintained their parent Legions' original names, badges and colours whilst the remaining Chapters took on new names and heraldry and eventually developed independent Chapter cultures, traditions and beliefs. The majority of these Second Founding Chapters still proudly serve the Imperium today.