Here's my theory:
Okay, so Mr. Krabs saw a hot whale while he was a sailor. They dated for a while, and everything was cool, until she wanted to settle down with him. After an argument, Mr. Krabs decided to get high, and then decided that he would ask for the (unnamed as of yet, although I want to say her name was Betty) whale's hand in marriage. She said yes, and they bought the anchor house Mr. Krabs has today.
He had made enough money to start his own restaurant, originally called the King Krab. One day, the two had a baby (Pearl), but things weren't so happy. You see, Mr. Krabs loves money, so he spent more time at work, until his wife bitched at him for doing so. He then killed her, but immediately regretted it. Not wanting to go to jail, he hid her body under the King Krab (although she was so big, it would take fifty King Krabs to cover her body, if the sand/sediment didn't already cover her). After that, he renamed the restaurant into the Krusty Krab, subtly noting that his heart was "krusty" with the loss of his beloved wife. In a bizarre twist of fate, to keep the body from being discovered, he puts a little bit of his wife's body in each krabby patty. That is the secret ingredient of the krabby patty, at the Krusty Krab.