I think Nautilus may be a demon or a cluster of demons feeding off of Nautilus'(The sailor) hatred for his crew in some sort of terrifying symbiotic relationship (you feed me all the hatred and suffering I need and I'll give you a tangible body to take your revenge type of deal). His appearance even matches the theory, he's a completely black void of shadows with glowing eyes much like that 
(Demon Shade) and 
.What do you think?
I think he's corrupted by the Void, we can see in 
's comic that the void also corrupts the depths and creatures from the sea.
Demons are different, they are shapeshifters, mind controller (Luring and taking control of your dreams) and they have to feed on humans pain/fear/despair
Is his lore up to date? While his main origin might not quite be there, I presume his involvement in the Harrowing is canon right?
This puts him on the side of good, to a degree. A demon like being wouldn't care about the inhabitants of an island. He's from Bilgewater, was investigating black ooze in the Guardian Sea. That black ooze was probably from the Void but he doesn't seem 'evil' or corrupted. So I think maybe he was saved by Nagakabouros. His lore stats he had few memories of himself but went back to Bilgewater, I think that process took hundreds of years as he wandered the bottom of the ocean.
