A jellyfish swims by SpongeBob's house, where SpongeBob and Patrick observe it out through a telescope. They prepare for jellyfishing, but then meet Squidward and ask him if he wants to join them. He refuses and decides to go bicycling instead. SpongeBob asks Squidward if he can join them next time. Squidward says yes and goes off. Unfortunately, while he is bicycling, he has an accident (involving a jellyfish) and is wheelchair bound. SpongeBob and Patrick decide that what Squidward needs is a "Best Day Ever" jellyfishing expedition. He isn't into it at first, but when a jellyfish stings him, he goes after it for revenge. He manages to catch the jellyfish, but in doing so angers a queen jellyfish. The queen jellyfish chases after him, attacking him with an extremely massive sting. The next day, SpongeBob and Patrick meet outside Squidward's house, and attempt to give a now life-support-bound Squidward the jellyfish that he caught the previous day. Squidward, still mad, opens the jar and lets the jellyfish attack SpongeBob and Patrick. As Squidward laughs, the royal giant discovers him and stings him, destroying his life-support. A completely blackened Squidward can only say, "Ow."
At the Krusty Krab, Squidward gives SpongeBob an order for a Krabby Patty. Spongebob begins making a show of cooking the patty, using his body to mix the ingredients together. After making the patty, it mysteriously "walks" out of the Krusty Krab. However, Mr. Krabs stops it, and pulls Plankton out of the patty. Mr. Krabs, unfazed by Plankton's attempt to steal the patty, puts him onto a plate, and throws it back to the Chum Bucket. SpongeBob has never heard of Plankton before, and Mr. Krabs explains to him that Plankton has been trying to steal the Krabby Patty formula for years, only to fail every time. That night, after the Krusty Krab closes, Plankton tries to befriend SpongeBob. He first claims that he and SpongeBob are friends, then gives the porous fry cook a golden spatula, telling him it's his birthday, hoping that all of these things will make SpongeBob more open to his request for a Krabby Patty and after he asks him for a patty, SpongeBob gasps, finally on to Plankton's game. He begins running away from Plankton, screaming "You'll never get a Krabby Patty from me! Even if we are friends! Never! Never!" But Plankton thinks otherwise, claiming that the "weak-minded fool" will hand deliver him a Krabby Patty personally. Later that night, after SpongeBob goes to bed, Plankton appears. He goes into SpongeBob's head, and navigates his way to SpongeBob's brain. He puts down a mysterious device that he's been carrying on his back, claiming that this "will be the end." SpongeBob then begins rolling around, his brain moving with him while crushing Plankton. After SpongeBob and the brain settle, Plankton tapes the brain to the floor of SpongeBob's head. He reveals a blueprint which contains his "highly elaborate and collage educated plan." The blueprint has an illustration of the device Plankton's carrying (labeled "Control"), with an arrow pointing to SpongeBob's brain, (labeled "Brain") Plankton puts the device into SpongeBob's brain and hits a large red button on the device labeled "Total Control." SpongeBob wakes up. Plankton then forces SpongeBob to get out of bed, and laughs fiendishly as he controls him. He forces SpongeBob to leave his pineapple home, forcing him to crash through the walls of the pineapple as he goes. SpongeBob tells his pet snail Gary that he'll see him later. Gary meows, and SpongeBob then realizes that something is wrong with him. He begins pleading his next door neighbor Squidward for help. Squidward ignores SpongeBob...until Plankton forces his victim to crash through the wall of Squidward's home screaming for help. Squidward begins yelling at SpongeBob, demanding an explanation. SpongeBob however, has gone noticeably silent. As SpongeBob begins going through the opposite side of Squidward's home, Squidward yells "Are you mad!?" Suddenly, SpongeBob turns 180 degrees at the waist, with a scowl on his face, and tells the "mediocre clarinet player" to shut his mouth in Plankton's voice. Inside SpongeBob's head, Plankton is using a microphone inside the poor sponge's head to speak through him and this causes his face to contort into a scowl. SpongeBob, realizing that something is wrong with his brain turns his eyeballs inside-out in order to see inside his head, and sees Plankton on top a device connected to his brain. SpongeBob yells "Get out of my head! Leave my brain alone!" "Never! Never!" Plankton replies, and forces SpongeBob to continue marching, laughing maniacally as Squidward faints. Plankton then forces SpongeBob to walk through the house of his best friend, Patrick. As he marches through, Patrick ends up on top of his head, and Plankton forces SpongeBob to throw him off. He then forces SpongeBob to crash through the Krusty Krab, and steal a Krabby Patty. SpongeBob, finally realizes his plan and begins screaming "No! NOOO!" as Plankton forces him to take it to the Chum Bucket. He marches SpongeBob through the Chum Bucket and stops him in his laboratory. Plankton forces SpongeBob to go to a machine at the lab's center. He tells SpongeBob that this is "The Analyzer," a machine that can describe the ingredients of anything put in it. He demonstrates by dropping a piece of seaweed into it. It crackles a bit, then says "Seaweed. 50% Sea, 50% weed". After demonstrating, he slowly forces SpongeBob to drop the patty. Before making SpongeBob drop the patty, Plankton asks him if he has any last words. SpongeBob, vainly struggles against Plankton's control, then apologizes to the Krabby Patty, and begins describing it's delicious features. Plankton, enticed by SpongeBob's description, jumps out of his head and attempts to take the Krabby Patty himself, but bounces off the patty and falls into the analyzer (which reveals him to be "1% evil, 99% hot gas"). Plankton is stuck in the machine and can't get out. SpongeBob, having saved the Krabby Patty (and thus the secret formula), says "Well patty, I guess we can go home now." Plankton begins screaming at SpongeBob as he leaves the lab, and the episode closes out with Plankton saying in a very humble, yet pathetic tone "I'll settle for some fries!"