Mr. Krabs tells SpongeBob to grab the secret ingredient to the formula from a S.W.A.T. truck driver, but to SpongeBob's horror, the ingredient isn't there. However, the only clue left on it is a small hole. So SpongeBob and Patrick go on a mission to find out who did it.
First, they suspect Plankton, since he is the only one that has ever tried to steal a Krabby Patty, but he asks if it is a joke, then to make him tell the truth, Patrick threatens him with clackers, still no answer. SpongeBob picks up the "Krabby Patty" and shows it to Plankton who then explains that he learned every ingredient but the secret ingredient and tested many ingredients to decipher the formula completely and was currently on raw sewage.
Next, they suspect Sandy (since SpongeBob suspected someone who is a scientist and engineer), who is storing Krabby Patties for the winter, but says she just bought them. SpongeBob's story of Sandy's crime was that she used an invisible potion to make her vanish, so nobody can see her. She then used her time-freezing invention to shoot a laser blast through the briefcase and take off, continuing the timeline again. She suggests that they should go and look at SpongeBob's house, so the boys suspect Gary.
SpongeBob suggests that Gary took a helicopter ride towards the delivery, so when SpongeBob kneels down to fix his socks and while everyone's distracted, Gary parachuted down and used his acid from his tear ducts to melt a hole big enough for him to grab the suitcase (SpongeBob later admits that he would never fix a loose sock during a secret delivery). Gary says he didn't do it, but he says he saw Squidward leaving the Krusty Krab with a black case. They interrogate Squidward, but when they open the case, they find it holds tap dancing shoes from a tap dancing contest, where he got third place.
SpongeBob goes back to the Krusty Krab and tells Mr. Krabs he cannot find it and who did it. Mr. Krabs then suspects SpongeBob (suggesting that SpongeBob used a decoy to look like he was picking up the delivery, then when everyone wasn't looking, SpongeBob swooped in, took the briefcase and then flew it over to the Chum Bucket where he sold it to Plankton for a quick buck) and calls the cops, but SpongeBob sees the secret ingredient in Mr. Krabs' hand. Mr. Krabs explains that the whole scheme was just to avoid paying $1.99 for the delivery. He is arrested and punished by forcibly giving away free patties for a day, while two officers hold on to his eyes to make him watch.
Judge Horace A. Whopper makes another appearance in this episode, despite this, he is referred to as Judge Trout. He first appeared in "The Krusty Sponge." He also has a Southern accent in this episode while he did not previously, but this must mean he has a doppelganger.
Those who were accused, and how they were:
Plankton: He had his own version of the Krabby Patty, but SpongeBob never explained how he could have stolen it. He was on raw sewage when SpongeBob came.
Sandy: She used an invisibility potion and snuck in, and used a time freezing ray, then used a laser to cut a hole in the case and get it. Sandy said that she legally bought over 283 Krabby Patties.
Gary: Gary snuck on to one of the choppers, and when SpongeBob stopped to tighten his socks, he shot acid out of his eyes, and stole the ingredient. It was deemed impossible by both of them. SpongeBob thought it was ridiculous for him to pull up his sock during the delivery, and Gary possibly thought it was impossible for him to shoot acid from his eyes.
Squidward: Gary said Squidward was walking out of the Krusty Krab with a black suitcase. Squidward shows them that the case contained his tap dancing shoes, in which he won third place in at a tap dance competition.
SpongeBob: Mr. Krabs thought that he set up a decoy, then swept down when no one was looking and stole it, then went to the Chum Bucket, and sold it to Plankton for a dollar.
Mr. Krabs: He was the one who stole it, because he didn't want to pay for it. Also, he makes SpongeBob blame four people all over Bikini Bottom so he would take the fall for it for his set up of the caper he made and attended him to do.
The guards never saw any of the accused in SpongeBob's stories.
It is revealed that Plankton had tried every ingredient from A to R in order to figure out the Krabby Patty formula; thus, the secret ingredient begins with a letter between R and Z.
Although Squidward has four feet, he only had two tap dancing shoes in the black case, though he is sometimes able to slip two feet in one shoe.
Sandy's receipt states that she bought 283 Krabby Patties which came to a total of $465.00. This would mean that each Krabby Patty cost approximately $1.64. That also means that her tax was 88 cents because $1.64 times 283 equals $464.12.
Plankton made some successful attempts to steal the Krabby Patty, awkwardly enough, it was in broad daylight. Also, he never used the Analyzer invention he made in the episode "Plankton!," and also that the Secret Ingredient is highly explosive.
The Secret Ingredient has to be bought, even if freshly made patties are used without sprinkling the Ingredient in.
There is another episode that comes later called "The Great Patty Caper," which are often confused. This is why "The Great Patty Caper" is also known as "Mystery With A Twistery."
Even if the Gary scenario was possible, the acid would have melted Gary's eyes; however, SpongeBob probably is not smart enough to know that.
This episode is considered, by some viewers, one of Mr. Krabs' worst moments (because he tried to frame SpongeBob for the theft).
Patrick is the only main character in the episode who was not accused.
The title card for this episode is similar to "Nasty Patty."
Also, both episodes feature a disgusting version of a Krabby Patty.
Mr. Krabs being forced to watch the Krabby Patties being given away is similar to the treatment in the movie A Clockwork Orange.
When SpongeBob is about to go into Sandy's home and puts on his helmet, it seems that when he is holding it in the air, it is already filled with water, which it should only be showing the helmet already filled with water in Sandy's dome.
When the red lights are flashing at the Krusty Krab, for a split-second you can see the background through the customers each time the red lights start to fade.
Whenever Gary meows, captions say that he is squeaking.
The security guard who gives SpongeBob the briefcase is first purple, but then he turns green when he tells SpongeBob to leave, but when SpongeBob runs, he is purple again.
Patrick puts two buns on the case. The bottom one should have fallen off, but never did, and in the next scene, the case is clean.
When Sandy comes down from her tree with her Krabby Patties, she comes down from the side when she could have just used her elevator inside her tree.
Water would have flooded Sandy's dome if SpongeBob were to dig a hole to get inside, unless the air prevented it from coming by maintaining its place in the dome.
When SpongeBob looks all around the case, there was no hole, but when he looked at it again, there was a hole. So the ingredient should've been there.
Gary says he saw Squidward with a mysterious black case, and SpongeBob and Patrick believe him, but the case holding the secret ingredient is brown, not black.
On the re-released version of the SpongeBob vs. The Big One DVD, it lists this episode as "The Patty Caper."
In Gary's story of Squidward leaving the Krusty Krab with a black briefcase, inside the Krusty Krab, there is a brown wooden background. However, the only room in the Krusty Krab that uses the brown wooden background is the dining area.