While SpongeBob is making Krabby Patties, he sings a song about how much he loves them, but stops in the middle and, while Squidward is stacking cups (in the form of a triangle), inhales air. Right after Squidward finishes the triangle of cups, SpongeBob (full of air) looks to his left and exhales all of the air, which wrecks the cup pyramid. Miss Gristlepuss then enters, and is unhappy with what she sees, causing her and her organization to ban Krabby Patties.
Mr. Krabs causes the Krusty Krab to be closed by threatening Miss Gristlepuss with a French fry strainer and insulting her by calling her a disgusting old prune. Meanwhile, Plankton at first thinks Mr. Krabs changed the name to "The Closed Krab," but soon figured out he could take advantage of the moment and went out to celebrate. Mr. Krabs' archenemy soon discovered in surprise that the Krusty Krab has secretly been reopened at SpongeBob's Pineapple. He threatens Patrick who was asking Plankton for the "password" while finding that his threats make up the password.
While Mr. Krabs was checking for cops, he goes to check on SpongeBob who was afraid of becoming arrested for making an illegal product. Mr. Krabs forces SpongeBob to work otherwise there would be weekends off. Plankton discovers Mr. Krabs is doing his regular business "under the table" and calls the cops. In the blink of an eye, they arrive to clean up the Krabby Patties and arrest the employees. Miss Gristlepuss trips and a Krabby Patty dropped into her mouth which made her love the sandwich and forgave the Krusty Crew, she decides not to send SpongeBob and Mr. Krabs to jail and unbanned Krabby Patties, she decides to reopen the Krusty Krab. Again, Plankton's plans failed and he hides inside one of the Krabby Patties only to be eaten by Miss Gristlepuss.
I can turn into a skyscraper!
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The Viking hat that Mr. Krabs wears when he greets T.U.O.O.F.A.T.T.A.F.A.D. was originally going to have a joke surrounding it. It would have been something to do with whom Mr. Krabs expected to be on the bus.
Andrea Martin's line were either recorded through the phone or in New York and was sent to Nickelodeon Animation Studio. The commentary this information comes from is not very clear on which it was.
Al Priss' design was based off casting director, Maryanne Dacey's late brother-in-law, whom was also a cop. It is implied that he died sometime before the episode premiered.
The Galley Grub was not seen in the Secret Krusty Krab. A probable explanation was that Mr. Krabs did not have time to write another one after his original one was still locked in the Krusty Krab.
The Secret Krusty Krab most likely made a rule in which there is a limit to the number of customers present within the building. This probably due to fire code or the building of Secret Krusty Krab isn't as wide as the regular Krusty Krab.
When SpongeBob is under his table, Mr. Krabs says that he will make SpongeBob take weekends off if he does not continue cooking Krabby Patties, but in "SB-129," he is off on Sunday, which is part of the weekend. Mr. Krabs must have meant the entire weekends.
If one were selling an illegal product in secret, it would be a dead-give away with a banner at the location in plain view.
Mr. Krabs and SpongeBob's hands were cuffed in front of them, when it should have been behind them.
The police cannot make a food illegal, as the police only enforce the law. It is the government that makes the laws. And even then it would take some time to get it passed (if it is even passed). While here, it only took one day to pass.
At the very end, "The End" card background looks very similar to the Season 9 title card for the episode "Sandy's Nutmare."
The scene where Plankton has to guess the password is based off a gag done by the Marx Brothers did, where they would make someone guess the password, which was "Swordfish."
When Squidward said "Do you want to 'Secret Size' that for $2 more" is a parody of McDonald's and their policy of allowing their customers to 'Super Size' their meal for more money.
The episode is heavily based off the Prohibition era in American History, which was a time when alcohol was illegal in America. The references are:
The banning of Krabby Patties is similar to the outlawing of alcohol
The Secret Krusty Krab is a references to Speakeasies, which were a place where people would secretly get alcohol.
The raid towards the end of the episode is a reference to the raids of speakeasies.
When SpongeBob had first started singing, there were four patties on the grill, later, there were eight.
Towards the end of SpongeBob's self inflation, the two spatulas he was gripping disappear.
When Mr. Krabs went to the cash register to Squidward for joking at Miss Gristlepuss and her sisters, he was standing behind the boat and his body was overlapping the cash register part.
When Mr. Krabs is seen greeting Miss Gristlepuss, the Krusty Krab door handles are blue instead of yellow.
Miss Gristlepuss blows her whistle and lets go, the black lanyard and whistle ends at her chest. But when the next scene cuts in her whistle is connected to the thread of her shirt without the black lanyard.
When Miss Gristlepuss meets Mr. Krabs, his belt was missing. In the next shot, he is wearing his belt.
On American airings, after Mr. Krabs meets Miss Gristlepuss, the closed-captions say "Mr. Grabs" instead of "Mr. Krabs."
When Plankton looks out his window to see the Krusty Krab, the road following to the Chum Bucket doors aren't there.
When Plankton asked Harold and Nat what was going on, he was wearing a suit. When he went up to SpongeBob's door and talked to Patrick, his suit was gone. It's possible Plankton took off his suit off-screen.
When the police are breaking into SpongeBob's house, Plankton is briefly seen hiding under a Krabby Patty. It is unknown why Plankton did not steal the Krabby Patty like usual.
It is possible that because the Krabby Patties were illegal, he did not want to steal it because he would have gotten arrested for selling them.
The Krabby Patty Plankton is seen hiding under has no seeds, unlike the other Krabby Patties.
When the Secret Krusty Krab was found by cops, SpongeBob and Mr. Krabs are handcuffed, but when Miss Gristlepuss accidentally falls down and eats a Krabby Patty, they are not handcuffed. Later, Mr. Krabs appears handcuffed again.