Board Thread:Warhammer 40k General Discussion/@comment-88.114.255.138-20130111160957/@comment-3258762-20130123220302

He defeated them. He didn't destroy them. It's like the Raven Guard on Istvaan V.

The reason for all the Warp Storms that wrecked the galaxy during the Age of Apostacy was because the 4 gods of Chaos united (Again) and tried to force their way into the realm of reality through the still not fully repaired Webway under the Golden Throne which Magnus destroyed. The Emperor met them in spirit and fought them off, thus saving the entire material universe.