I think it always *used* to be the Emperor, becasue in the intro cinematic from eons ago, you see a far more elaborate Flayer Armor, very similar to that which the Emperor wears. Now, back then he was probably the OG Illithid Emperor and it suddenly makes sense that he goes to find a band of heroes to control, infiltrate the human world and free the Elder Brain.
However. If you do the Speak-With-Dead thing on the Flayer that lies Dror Ragzlin - The Hobgoblin leader in the Gobbo base - he tells you he was the one responsible.
