There is a scrawled drawing in blood in several places (wall by Wakeem's Rest, and several shields found in Shattered Sanctuary) showing five stalks firing approximately straight up around a central thing that looks like an eyeball. To me, that has a LOT of reminders of the old "Dragonlance" story line, where Tiamat was renamed and took the form of a woman with five strands of hair in the form of each one of the chromatic dragons. My thinking is that, for whatever reason, the mind flayers attacked Tiamat's domain in hell and are having their asses handed to them. So the mind flayers are attacking human settlements as a kind of forced recruitment in order to staunch their military losses.
My theory of events explains Raphael coming into your camp with his "offer" (I literally said to myself "that's a devil" almost the moment it showed up); "he" was dispatched by Tiamat with the offer to basically not recharge enemy forces while simultaneously grabbing a few servants of her own. It explains the woman that came to "save" me from Priestess Gut from out of nowhere as well. That could have been Tiamat, or it could have been another devil/demon-kind under Tiamat's service. It also explains why the Mind flayer ship could so easily transport into Hell to begin with: the mind flayers were trying to control the front line and force that front line to be in Tiamat's domain. Not smart, but if you can show up on your enemy's doorstep at will, it's hard for your enemy to advance their forces onto your domain.
Still haven't figured out why the Githyanki are involved other than they want to be the big, psionic bullies on the block and the mind flayers get in the way of that. In the original, opening cinematic, I thought the dragons being ridden were bronze, which made me ask why the Githyanki are on Bronze dragons (mind control, I concluded), but I also can easily believe that those were very tiny red dragons, as well. Or that is a very large ship.
More practically, Tiamat is a very recognizable figure in D&D, to the point where she appears in multiple locations/mythos in the game, and, frankly, I'm a little surprised (especially after the old Dragonlance campaign from way back there) that Tiamat isn't considered an actual deity at this point. I think she made an appearance in Neverwinter Nights as well (again, old game), but I don't remember that one for absolute certain (no pun intended).
It could be that the Absolute is also some kind of Githyanki deity, but I don't have as much evidence for that one.
Anyway, that's my two cents: The mind flayers are at war with Tiamat.
