In the Great Scouring the Imperium of Man blew up the foul traitor forces that were left over from the Horus Heresy, herding them into the Eye of Terror instead of finishing them off. During the fighting, various Xenos seeking revenge or conquest tried to attack the Imperium, but the psychotically furious loyalists destroyed most attackers in the crossfire. Foaming at the mouth fanatics don't use weapons of last resort as a last resort, after all. Well, not yet.
It is a period of the timeline that doesn't have a lot of fluff for it at the moment as little was known about it before the Horus Heresy series of books began and the writers are still working their way up the siege of terra at the moment. Hopefully once Dan Abnett has written the epic that is the Emperor bitch-blasting Horus into a million soul fragments we will see a lot of writing about this period of the history and close out the leftover Horus Heresy plotlines and detail the fates of characters.
According to Cypher many of the "foul traitor forces" were members of the nine loyalist legions, leftover Horus sympathizers and other Chaos marines who were rooted out with extreme prejudice. Granted, this is part of a "the reason you all suck" speech about the Dark Angels, telling them if they had just admitted to the Fallen existing during the Great Scouring they wouldn't be stuck being "the Unforgiven" so many thousands of years later. So take it with a grain of salt. Though, it very much is likely that The Scouring had a strong aspect of rooting out and purging any Chaotic or rebel sympathizers. Likely anything that didn't strictly toe the line of Compliance was ruthlessly annihilated.