A/N: Just a little heads up, plenty of things happen in between each movie.
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A group of soldiers, led by Rex Raptor, another one of Yugi Muto's archenemies, has infiltrated, restarted, and reopened Plankton's old restaurant, The Chum Bucket. However, the restart has also inadvertently restarted one of Plankton's old inventions, the Duplicatotron 3000, a machine that produces an army of robots to use to steal the Krabby Patty Secret Formula. After restarting the machine, Rex initially thinks that this could benefit Weevil, but realizes that the switch on the Duplicatotron's Obey Setting is still set to "Off" (An old mistake that Plankton once made when he first made the machine), and the robots quickly escape through the Super Portal that Rex used to enter SpongeBob's world.
A month and a half later, SpongeBob, Patrick, Tai, Sora, Izzy, TK, Kari, and Davis are delivering a truckload 1,000 Krabby Patties to a newly made factory, which, unbeknownst to them, is being operated some of the escaped robots, who have been quickly evolving. Upon arriving at the factory, a robot guard sucks up all the Krabby Patties. As Patrick, Davis, and TK try to help the guard slow the vacuum down, they unintentionally get sucked in as well in the process. SpongeBob, Tai, Sora, Izzy, and Kari chase after the robot guard, but are blocked out. However, they eventually find their way into the factory after SpongeBob disguises himself as a worker robot, which had been recently rejected after a defection.
After finding their way through the factory, SpongeBob, Tai, Sora, Izzy, and Kari find Patrick, Davis, and TK vacuum-packed like toys. After freeing them, they encounter Yugi, who claims to have been abducted and scanned. They later find Téa, along with an ill Joey and Tristan, who also claim to have been abducted and scanned. After searching the factory, the heroes discover that all of the Duelists in Yugi's home, and other cities are being abducted and scanned for a much bigger plan by the robots. So, the heroes have no choice to save them.
Among the captured Duelists are Jaden Yuki, Yusei Fudo, Akiza Izinski, Yuma Tsukumo, and Yuya Sakaki, who are all locked inside cages. The heroes work their way through Bikini Bottom, splitting into different groups: SpongeBob and Tai in Downtown, Patrick and Davis at the Flying Dutchman's Graveyard, Sora and Kari in the Kelp Forest, Izzy and TK at the Mermalair, and Yugi and Téa at Bikini Bottom's Hydrogen Labs to locate them and various objects stolen by the robots. To free them from captivity, they play a game show-style trivia game where they must score 500 points to free the Duelist from the cage. Then, they continue to find the remaining objects and battle the remaining robots. Once all the items are collected, they return the items to their rightful owners.
After the heroes gain access to the Chum Bucket, they discover a giant robot Black Luster Soldier, named Black Luster Titan, and the revived Robot Plankton and learn that Rex and his cronies were responsible for reactivating the robots. SpongeBob manages to destroy all the green weak points, but Robot Plankton revives the Black Luster Titan, kidnaps Kari, and enters the brain, with SpongeBob in pursuit. Inside, SpongeBob manages to disable Black Luster Titan's brain and rescues Kari from Robot Plankton. After all three escape the brain, Black Luster Titan falls to pieces. Robot Plankton still has the Duplicatotron, but it produces several more Robot Planktons, who, unlike the last time they appeared, proceed to dismantle a frantic Robot Plankton. As the clones dismantle the prime, SpongeBob hopes that Rex learned his "lesson", but instead of a response, Rex rudely exits The Chum Bucket. The movie ends with the heroes exiting as well to handle the remaining robots that are running amok in the city.
In the post-credits scene, a young brunette girl watches the sunrise on a hill where her entire hometown can be seen, wondering why she's "hearing strange sounds coming from the ocean".
