According to most theories, it has become most probable to people that The Great Unknown is actully the Bombinating Beast from Lemony Snickets more later series “All the Wrong Questions” on the loose, apparantly free.

I thought the Bombinating Beast and the Great Unknown were both like, the dad of Ink or something. Ink went to try and save the population of the island with an apple, that's where he went. Since the Great Unknown appears to be some sort of giant sea monster and Ink is a snake that can swim well, I figured that the Great Unknown was a member of the same species but much older, so a giant sea serpent or something. That's what I always figured.

I agree, it must belong in the same species but older. Except if it’s nothing but a metaphor.

Well, in The End Kit says that they encountered the Great Unknown and she escaped with the Incredibly Deadly Viper, and it couldn't be in two places at once. Perhaps they are related but I don't think they are the same thing.