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?
I thusfar suspected Gale for being responsible for that, but I have no other reason to think that, besides; "A Wizard did it" - Oh, and tht he mentioned me lying somewhere, so he thought I was dead. He could of course mean, on the ship itself.
I have a suspicion Gale was never on the nautiloid.
Gale is an origin character, which means if you choose to play him he goes through the whole nautaloid prologue sequence, and is the one saved by the mysterious force.