So I been watching a lot of SpongeBob in the last little while (my kids love it) and I found out what the Krabby Pattie secret formula is. Mr. Krabs has a whale daughter. But her mother is never shown (or referenced). Mr Krabs makes reference to driving a taxi and being in the Navy before opening the Krusty Krab. My theory is that the Krabby Pattie is in fact Pearls mother, and his wife. There is never any reference to her within the show. Maybe she wanted to divorce the greedy crab and he couldnt handle having to pay after the divorce was finalized. Therefore he killed her and decided to hid it by freezing her and selling the meat in his restaurant. A whale can produce a mass amount of meat for the tiny town.
Whenever Plankton tries to steal the recipe Krabs uses everything in his power to stop him. The main reason isn't to not only to keep him learning the grisly truth but also to keep his daughter safe. Plankton is evil, once he learns the secret formula to a Krabby Pattie, Plankton would do nothing but want to make them. There is only 1 whale left in Bikini Bottom.. Krabs daughter Pearl.
Plus... it hamburger right. There's no cows under sea. Therefore it's whale meat.