Also, the campaign would start with you choosing what key Elder Brain to strike first. The options in my mind for starters are:
-Celestia Pool: Once the Mind flayers figured out how to turn off the local sun, the silver sea is a wonderful place for growing their tadpoles in mass, along with other experiments that demand lots of liquid. Bahamut's skeleton has been turned into a theme park.
-Ysgard Bio-lab complex: where the Mind Flayers perform their greatest experiments in breeding of new mutant species, taking advantage of all the extra vitality around. You can also eat somebody's brain and it will regenerate the next!
-Mechanus Thoon factories: churning out the latest mind flayer technologies for the last decades. Now with at least 20% organic and bio-degradable components!
-Acheron Arena: where the Mind Flayers drill their armies against each other, as well as holding skirmish competitions between elite teams and duels between champions that are broadcast to all the other planes. Glory and gold for the winners! Humiliation for the losers! All the adrenaline around gives the brains an exquisite taste.
And in all of those Mind Flayers have transported around slaves of numerous races from other places, so you never know who or what you may find anywhere.