According to the lore vids I watched while waiting for EA release, Mindflayers have a kinda prophecy about a ceremorphisis that goes wrong and creates an independent Mindflayer with the memories and thoughts of its original host.
I would totally do an evil play through if it culminated in the tadpole and player agreeing to coop the process and become their own thing...a Mindflayer that still possesses the soul of its host.