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The game begins with SpongeBob and Patrick playing with their robot toys. The former wishes that the robots would come to life.
Meanwhile, in the Chum Bucket, Plankton has planned on creating a robot army and use them to take over the world. Not only that, he will also achieve in getting the Krabby Patty formula. Plankton has created a device called the Duplicatotron 3000, a device used to spawn robots. Unfortunately for him, the robots disobey him because the switch is on disobey. Because of that, Plankton is kicked out of the Chum Bucket.
SpongeBob wakes up in the next morning to see his house has been trashed. When he goes outside, he sees Plankton. The latter makes lies to SpongeBob that robots came out of nowhere and wrecking havoc in Bikini Bottom. Fooled by this, SpongeBob plans to stop the robots.
By the time he and his friend go to the Chum Bucket, SpongeBob has finally discovered that Plankton is behind the entire plot. He admits that he is planning on using a robot army for his purposes. When SpongeBob tells him that his robots are causing a rampage, Plankton tells him that it is because the switch to his device is on disobey method and tries to get the robots to his command. Unfortunately, a robotic version of himself refuses to allow that and sends a gigantic SpongeBob robot to deal with SpongeBob which he defeats both of them.