The response of Magnus' new patron was immediate. The City of Light was transported into the to a new that had already been prepared for its new occupants. Prospero was destroyed that day, but Magnus and his Legion survived. By the time the Thousand Sons were seen next, they had joined up with Horus' force of Traitor Legions on their way to lay siege to Terra, and Magnus the Red had become the most powerful of all Tzeentch's daemonic servants, the first of the .
After the Emperor defeated Horus on his flagship the at the end of the and the Traitor Legions fled from Terra, the Thousand Sons returned to the Daemon World that Tzeentch had prepared for them within the called the , that was complete with a twisted, Chaotic caricature of the city of Tizca. Tzeentch had another "gift" for the Thousand Sons, namely the full return of their aberrant genetic mutations, which threatened to turn all of the surviving Thousand Sons Chaos Space Marines into mindless . A number of high-ranking officers of the Traitor Legion, lead by the Sorcerer , who had been Magnus' closest advisor since their Legion's earliest days, established a secret Council of Sorcerers to find ways of stopping the mutations. With Ahriman at the fore, these sorcerers eventually invoked a powerful sorcerous incantation that backfired, killing all those Astares of the Legion who lacked psychic abilities and transforming them into living automatons: their organic bodies turned to ash, while their unknowing spirits were trapped within their suits of , which were hermetically sealed and fully animated by their trapped souls. Every joint of the armour was magically sealed, and the only way for the soul to escape this prison was for the armour to be destroyed. The minority of Thousand Sons Astartes who did not succumb to the spell later known as the found their psychic Warp powers increased to a tremendous degree. The ritual also accomplished its goal, for the mutations stopped, both in the surviving Sorcerers and their undead brethren. Magnus was enraged by the outcome of the spell and what it had done to his Astartes and became determined to gain vengeance upon Ahriman and his cabal of rogue Sorcerers.
As I alluded to, the real big changes came earlier for the Thousand Sons. 6th edition boosted Thousand Sons with the changes to Fearless and Cover saves.