Isaac Hayes (Chef) quit because of an episode called Trapped in the Closet lampooning Tom Cruise and Scientology as a ludicrous cheap science fiction like fraud of a religion. Tom Cruse reportedly threatened to stop promoting MI3 if Viacom (Comedy Central’s parent) re-ran it.
So South Park created a final episode called Chef Returns out of obviously spliced together clips of Chef’s words over the years where he returned from being brainwashed by a cult of child molesters posing as big game hunters. In the end, Chef couldn’t get out from under their spell, fell down a cliff trying to escape and the had his face and body graphically torn apart and eaten by wild animals.
On second thought, that’s pretty ambiguous. They should have come out more strongly against Scientology.
Of course I'm joking.