For that the main character would have to transform into an ulitharid, then go live in a mind-flayer colony for a bit and then could decide to take half the colony and go set up a new colony elsewhere with the ulitharid becoming a new elder brain. Technically not impossible or even insanely unlikely should our character undergo ceremorphosis(1-4% chance of turning into an ulitharid) but I really don't think the game will go there. That would just completely derail the story. Even if we are allowed to play as a mind flayer/ulitharid I don't think the game will go down the path to becoming an elder brain.