Plot
B.O.O.T.S. (Bureau Of Official Texas Science) Laboratory in Galveston, Texas, where Sandy Cheeks works, scoops Bikini Bottom and its inhabitants out of the ocean. Confused about their possible motives, Sandy and SpongeBob SquarePants go to the surface to return Bikini Bottom to the ocean floor, but are blown off course by a tornado after hitching a ride on an airplane to reach B.O.O.T.S.
At B.O.O.T.S., Mr. Krabs goes outside to see what is going on and is surprised to see a human woman; Phoebe, one of Sandy's closest colleagues at B.O.O.T.S. along with Kyle. After discovering that Sandy and SpongeBob were not captured, Sue Nahmee, the new head of B.O.O.T.S., demands that they capture them as soon as possible.
During a fight with a gang of rattlesnakes, one of them bites Sandy and she calls upon her family, who work as a traveling circus act, for help, and they agree to bring them to B.O.O.T.S. At B.O.O.T.S., Sue explains her plan to genetically modify the people of Bikini Bottom to breathe air and then clone them to sell as toy pets, experimenting on Mr. Krabs, Squidward and Patrick to test how well children will enjoy playing with them.
While Sandy's brother, Randy, shows SpongeBob how to do the Cheeks family whistle, the family gets into a car chase with the police because Randy used their van to illegally smuggle nuts. While they fend them off with the tornado, it does not work; as a last resort, SpongeBob and Sandy are launched out of a cannon to B.O.O.T.S. At the water park, Cuda, Sue Nahmee's pet pug, pursues them into the sewers, which leads to B.O.O.T.S. Sandy learns of Sue's plans and tries to attack her, but Sue puts her in a cage with a hamster wheel while SpongeBob is put on a roller coaster ride leading to the cloning chamber. Sue then rips off her lab outfit, and it is revealed that her neck was made of rubber, and peels off with her necklace in a flash. She is then revealed to have a cyborg body, masquerading as a human, with no neck. She explains that she was motivated by the desire to cuddle with fish, which she could not do because fish die when out of water. She also reveals that she used Sandy's life in Bikini Bottom to spy on its inhabitants, causing everyone to feel betrayed. SpongeBob arrives in the cloning chamber and is popped and divided into thousands of tiny versions of himself.
One of the tiny SpongeBobs motivates Sandy, telling her not to give up on saving Bikini Bottom. Sandy escapes from the cage and confronts Sue, who is defeated after she is decapitated and her head is fed to her pet fish. Mr. Krabs discovers that fusing the tiny SpongeBobs together will return SpongeBob to normal, and he, Squidward, and Patrick work together to bring him back. However, the stand holding the glass orb containing Bikini Bottom collapses itself over, and the orb cracks, causing all of the water to leak out. Sandy tries to call her family for help using the whistle, but is unable to because she lost a tooth while fighting Sue. Having learned the whistle himself, SpongeBob calls upon them to help rig a mechanism to launch Bikini Bottom back into the ocean. With Bikini Bottom back in place, everyone celebrates by having the Cheeks family circus perform at the Krusty Krab, by singing a song.
