Thanks guys! Yea, this would be a preety daring feat to make this idea a reality, but if anyone would create this, i would be happy to take some time to edit the animations!
Heres a quick sketch of the would be first boss, Omega Nautilus:

How you would beat him: The yellow pipe on his shell plays a note and emits a certain color, if you match the note with your song, he moves forward a bit, he lashes his tentacles as an attack, eventually, you lure his far enough, and he falls into a chasm, and his falling body destroys a rock wall, opening an exit, when you swim out a cutscene begins:
Guardian: As I swim near the fallen behemoth, I feel a strange force engulf me, and i hear the beasts voice in my mind. (even though jellyfish dont have brains)
Omega: You are stong, small one, and you have freed me from the binds of evil, for that, i will give you something in return. now, i must die...
Guardian: I thanked the creature as its voice faded, but i felt a spark inside me, something new, but at the same time, i wondered what it meant be binds of evil. I now felt a piece of the creature inside me, I could now change guises into a Nautilus.