The intro of the game shows Professor Calamitous in a game explaining that by feeding fairies with Krabby Patties, they can emit gas, combined with ghost energy, can be used as a fuel for his army of Toybots. Just then, he uses a Toybot to attack the host of the show.
Just then, in Bikini Bottom, SpongeBob and Patrick are delivering Krabby Patties to a Krabby Patty Processing and Toybot Factory. Upon arriving there, a robot sucks up all of the Krabby Patties and Patrick. SpongeBob goes through the factory to rescue him.
He frees Patrick and meets up with Tak, who happens to be abducted and scanned. Upon meeting Jimmy and Timmy, they also have the same fate.
They meet up with the Chad Bot, a robot who is Calamitous' helper. He orders them to find master models for his collection. Also, Jorgen Von Strangle assign them to free the fairies.
After all of this, they confront Calamitous and defeat him.