After being unsuccessful yet again at stealing the Krabby Patty secret formula, Plankton returns to the Chum Bucket, feeling dejected, when he becomes surprised to discover that his computer wife Karen has transformed the Chum Bucket into a successful Mexican-chum restaurant. Plankton becomes agitated at Karen’s plan being not evil centric and burns the place to the ground. Karen becomes annoyed at Plankton never supporting her ideas and removes one of her empathy chip and starts to use magnets to invent a gigantic floating fortress and take control of the world.

Plankton becomes worried about what Karen is doing and enlists SpongeBob to help support him. SpongeBob uses his hypnotic skills to help Plankton reach the same page as Karen, where he reveals that he found Karen as a calculator back in the day, connected to a potato in a petri dish and when Plankton went to the Bikini State University, he upgraded Karen to her current form. Together, the pair build a freeze ray and plan to take over the planet. Their original plan failed when a human child found them on the beach and threw them back to the ocean floor. Plankton overheard Mr Krabs saying that the Krabby Patty secret formula was what would help him take over the world and that is the reason Plankton was trying to steal it all these times.

The pair head back to the University to find some of Karen’s original body parts and Plankton uses them to build a new mech, in a bid to destroy the current one. Unfortunately for Plankton, Karen merges into the mech body. Plankton refuses to take responsibility for his actions, which greatly annoys SpongeBob, so he takes Plankton to visit the Gal Pals consisting of Sandy, Pearl and Mrs Puff. Together the Gal Pals insert Karen’s empathy chip into Planktons brain and he begins to see and feel what Karen did about him. The Quintet rush over to stop Karen, by infiltrating her airship.

Karen fights the Gal Pals by disconnecting from the other versions of herself whilst Plankton tries to reconcile with his wife. SpongeBob and Patrick cook potatoes to use as the ships source of fuel. Karen plans to reject Planktons offer of winning her back by handing him the secret formula, but Plankton tells her that she is the one true formula he needs and the duo join forces once more and attempt to take over the world together again. Unfortunately, Patrick eats all of the spare potatoes, causing the mech to crumble before collapsing, thus restoring Bikini Bottom back to the way it was before.

Back in the normal town of Bikini Bottom, everyone wants to tread on Plankton and Karen, before SpongeBob stops the townsfolk and admits that he was moved by Karen and Planktons love story, which ultimately causes the townsfolk to agree and they all throw a party in celebration.