The subjugated elder brain is an interesting concept.
What if the illithids who captured the player character are trying to save the elder brain in question by making the player being their pawn to join the absolute and discover what's going on and where it is located? It would explain why the tadpole is dormant.
I doubt this, the Flayer onboard the Nautiloid thinks you are his thrall, after all.
But he's the one who put the tadpole inside your head. So are you suggesting he doesn't know it's a special tadpole which has a different purpose than the ones they usually use?
Maybe the (totally not a DOS2 repeat) scene at the end of the intro where a mysterious force saves you from dying is supposed to imply the shadow magic being inserted into the tadpole?
Raphael is the entity that makes the most sense to have saved you. He send someone to save you later in the game if you take a certain path with Priestess Gut and fail some rolls (or just don't take them) even if you haven't meet him first.
