The game centers on another one of Plankton's evil schemes to obtain the Krabby Patty secret formula. In his attempt to do so, Plankton commands an army of sea ants to assistant Robot Krabs in order to retrieve the Krabby Patties in the robot, only to realize he made a fatal error that now has it going on a rampage. Can SpongeBob save the day even after thinking he is the cause of the mess? Plankton has hidden Gary and in order for SpongeBob to find him, he must complete missions hosted by Plankton, but it is really a trick to get the Krabby Patty secret formula.
The plot storyline of the wrong side is that Gary is kidnapped by Plankton, and Plankton uses SpongeBob as a victim to get Krabby Patties from him or pay 100 dollars to get Gary back. However, because of a malfunction in change of a tape-recorder plot, Plankton can only steal Krabby Patties made by himself, using an army of red sea ants to get them. But first, Plankton will make SpongeBob get him a whole list of items that are not useful.
Plankton hires red sea ants to capture Krabby Patties in a Robot Krabs from "Imitation Krabs." Just as that happens, the red sea ants are successful as they can easily steal all the Krabby Patties when lazy Squidward sleeps. When Squidward wakes up, SpongeBob sees Robo-Krabs out, and now the Robo-Krabs is out of control! Plankton cannot control it right now! SpongeBob must get his driver's license, then must catch cheese because Patrick has him persuaded from the hooks in "Hooky." Then, he runs into Sandy Cheeks after he finds Robo-Krabs again, but Sandy tells SpongeBob she needs help to collect some jellyfish jam, so SpongeBob has to help her. After that, SpongeBob finds himself in Mr. Krabs' ship and pirates are stealing the riches from the ship! SpongeBob then has to bubble the pirates away from Mr. Krabs' treasure, and Robo-Krabs tries to aim a cannon at SpongeBob, but Robo-Krabs, at an uncontrollable situation explodes with no reason. Plankton seeks revenge with a MORE highly-college educated plan to steal the Krabby Patty formula!
In the PC game Employee of the Month, there is a poster of Operation Krabby Patty's cover art, which is named "America's Favorite Sponge." If one clicks on the poster, SpongeBob breaks the fourth wall and says, "Ooo! Operation Krabby Patty! That was my very first game... good times, good times."
Technically, this is not true because Legend of the Lost Spatula was the first SpongeBob game to be released, and in Europe, SuperSponge also came out before-hand. However, Operation Krabby Patty was the first SpongeBob PC game.
Mermaid Man and Barnacle Boy make a cameo in the video game part Boating School #101 and has a picture signed with an autograph.
The wrong side has several typos, such as "Min Menu" instead of "Main Menu."
The mail delivery service FedOh is a parody of FedEx.
The red sea ants Plankton hires resemble big-brain sized aliens from American films like Mars Attacks!
The three red sea ants that are talking to Plankton separate when they are trying to make sure what to do were wearing cowboy hats and scuffs.
Plankton was corrected that there is no such thing as a "hundred gazillion dollars" by the radio-connection reader.
The fourth wall is broken when Plankton politely asks the artist to put the elevator in the correct location with a paintbrush visible.
In the Wrong Side intro to Boating School 101, Plankton tells SpongeBob that if he successfully completes a mission for a clue as to Gary's whereabouts, he says that SpongeBob will gain immunity and cannot be voted off. This is a reference to the hit reality TV series Survivor.
Jellyfish, wrong stoplight checkings, hooks with no cheese, the Flying Dutchman's green fireballs, and electrical eels give the player a time penalty.