Cartoon Theories

The Marvelous Misadventures of Flapjack

This chapter is dedicated to @Klover2319

The little old lady is related to Flapjack
Most likely his grandmother. Obviously, this implies that Flapjack's parents either abandoned the pair of them or are dead.
Stormalong rests directly atop the ruins of Candied Island.
Which is why nobody ever finds it!
Jossed, in the episode Over the Moon it's shown that Candied Island is real.
Bubbie murdered Flapjack's real parents.
Think about it. Bubbie was hesitant to answer Flapjack's question (if Bubbie remembered where he came from) in the episode "Oh Brother!" She told Flapjack a story about finding baby Flapjack in a bed of seaweed which, given the crappy world the characters inhabit, seems improbably idealistic. More likely, Bubbie was covering up the truth that she very badly wanted a child but for some reason couldn't have one, and she somehow killed Flapjack's parents (likely by smashing their boat) and taking baby Flapjack to raise as her own.
Additionally, in another episode, Bubby mentions her "babies", as in plural. One can infer that Bubby has "adopted" other children in the past, who have grown up and moved out. K'Nuckles may be one of these, and is possibly the Stormalong equivalent of a grown man living in his mother's basement. Additionally, we never see any other whales on the show; due to extensive whaling, Bubby may be the last of her kind and in a state of denial, adopting and raising human children in a futile attempt to "save her species".
We do see another whale, one who kidnaps kids from their guardian animals and makes them work on his laundry island. She may be the last female whale though.
Possible reasons that Bubbie would be childless: She's barren, she's considered unattractive by whale standards, she's a Christmas Cake, or she has some position in whale society that prevents such things. None of these things are contradictory. Therefore, all of them are the case.
And considering how uncomfortable she got when Flapjack talked about squishing people because she's so big...
Alternately, Bubbie was telling the truth and the reason Flapjack was found in a pile of seaweed is because he's one among many children of Poseidon himself. He was presumably dumped there by Poseidon who wanted nothing to do with him or maybe his mother died in sea trying to protect her child from him. The reason Flapjack is mortal is simply the results of Gods screwing around with mortal women (granted, that would make Flapjack half God, but that's another theory altogether). Perhaps Bubbie's hesitation to tell Flapjack the "truth of his birth" is fear he'd one day get the wise idea to leave her and seek his true parents.
Or, Flapjack was born on Titanic.

via tvtropes.org