When I was thinking about some parts of Nautilus' dialogue mentioning King Amidias, it made me consider the fact that King Amidias is trapped within the Giant Clam in new Calamity worlds. With this information, I feel like the creatures that killed everyone but the king and Nautilus were the clams from the Sunken Sea, with the latter taking refugee in a enclosed area in the underground desert. Once the Giant Clam is defeated by us, Nautilus isn't aware that the king is still alive after all these years no matter how much we interact with them. Then again, Calamity Fables isn't supposed to be played with the OG version together at the same time so feel free to prove my headcanon wrong and to take this with a grain of salt.