SpongeBob hasn't done his science project, so he wishes he was in the greatest laboratory in Bikini Bottom and thus ends up in Sandy's lab. Using an Auto-Poofer given to him by Patrick and Sandy, he goes back to his own room. He wishes he was in the greatest lab in the multiverse. SpongeBob (now in LEGO) arrives in Unikingdom in Dr. Fox's lab. Jimmy, who can be seen currently, is updating when SpongeBob drops in and starts to mess with her inventions. Unikitty accidentally uses SpongeBob's Auto-Poofer, causing her to disappear to Bikini Bottom. Seeing Goddard, Timmy mistakes him for a game console, where Timmy puts in a video game he was carrying which causes Goddard to become more like the violent Decimator game.
Just then, Puppycorn and Dr. Fox drop by and mistake SpongeBob for Unikitty due to Puppycron believing Unikitty has shrunk her own head. The two then start to use the absent Unikitty to play with her unguarded inventions.
Back in Bikini Bottom, Unikitty (now in 2-D), finds herself in SpongeBob's room and meets Patrick and Squidward, who (for their sake) she believes to be creatures. However, Vicky, and several kids in Timmy's school stupidly believe Unikitty to be SpongeBob using a costume to make up for not doing his science project. Unikitty inadvertently uses the Auto-Poofer in front of Mrs. Puff who realizes that he has found a way to get into Fairy World. Jimmy ends up back in SpongeBob's room and after finding it only teleports her there, combines it with SpongeBob's handheld video game, so she can teleport anywhere. After tracking Unikitty to SpongeBob's home, Mrs. Puff steals Unikitty's device before she can use it, and teleports her, Unikitty, Cosmo and Wanda, Zim, Wubbzy and many more charaters to Fairy World.
Back in Unikingdom, SpongeBob and Dr. Fox enjoy hanging out with each other at the Park, but a robot of her appears, now taking on the form of the Decimator. After Timmy blows it off at first, Libby, Carl and Sheen try to stop the giant robot from destroying the town, but fail. Meanwhile, Timmy and Cindy are on a date trying out all of Jimmy's inventions. Timmy asks Cindy if she'd still like him if he wasn't a genius, but Cindy answers no. Carl, Sheen, and Libby run to Timmy and warn them that Goddard is after them, but Timmy STILL doesn't care and thinks it's not a big deal. Goddard arrives and shoots the kids with flames, though they remain unharmed, just black with soot. Timmy realizes what he has done. He tries to get home to Cosmo and Wanda for help. But before he can escape, he is eaten by the Decimator. Goddard targets the Purple Flurp factory and decides to destroy it. Libby tells everyone if he destroys it he'll cause a major flurp spill, which could dissolve all of Retroville (what with the acid and corrosive sugar in the Flurp). Libby calls Cindy and Timmy to warn them. Realizing they have no time to get to the core, Cindy figures out that if Timmy disconnects the game's overdrive, the game will shut down and Goddard will deactivate. However, the laser pen runs out of power, so Timmy uses his teeth to bite through the system. With time running out for Timmy, just as Goddard is about to destroy the town with his rockets, with Cindy's help, manages to shut down Goddard, and restore him to normal. Cindy arrives in Jimmy's hover-craft. Fortunately for Timmy, Cindy stupidly believes that Timmy created the evil Goddard so that she could solve the entire incident, and she kisses him, much to the other's disgust. With Goddard back to normal, Jimmy makes contact with his friends and informs Timmy that Crocker is in Fairy World.
In Fairy World, Unikitty comes in contact with SpongeBob, who is alarmed to find out that Mrs Puff is in Fairy World. Unikitty does not listen to SpongeBob's plan to get Mrs. Puff out of Fairy World and refuses to help him after the trouble Timmy caused. Mrs. Puff then discovers that if she stole magical equipment and knocked down the Big Wand (which powers the fairies' magic); the fairies would surrender to him. Puff steals a suit of magical equipment and knocks down the Big Wand, making all the fairies, including Cosmo, Wanda and Jorgen von Strangle and other characters powerless. Thinking the fairies to be unreal, Unikitty then gets ready to leave after stealing the Auto-Poofer from Crocker. After talking with Timmy, who convinces Unikitty that Cosmo and Wanda are as real to SpongeBob as Goddard is to him, Jimmy makes his Brain Blast and has planned to stop Crocker. Returning to the school, Unikitty combines the science fair entries into a robot which Cosmo and Wanda used to distract Crocker. Using the robotic decoy in suit to distract Crocker, Jimmy repairs the Big Wand so that the fairies' magic works again and Crocker would be defeated. Jimmy, using Jorgen's wand, makes Crocker's suit vulnerable to magic and turns Crocker into various scientific equipment, before making him powerless again. Crocker is attacked by Jorgen, who makes Crocker lose all memory of Fairy World. With the fairies' magic restored, Timmy wishes that Jimmy, and he could get back into their own hometowns. The two shake hands in the area between both of their worlds, which causes Timmy to be back in 2-D and Jimmy to be back in CGI. Cindy shouts that she'll never forget him, while Jimmy tells her to leave his lab.
Back in Dimmsdale, Principal Waxelplax reveals that she would be judging the science fair instead of Crocker, who she claims has lost his memory “in a bizarre schnauzer incident”, causing Crocker to go insane upon hearing the word “schnauzer”. Cosmo and Wanda note what a good day they've had, before SpongBob reminds them that he still hasn't finished his science project. Out of a wormhole appears Goddard (now in a 2-D/CGI form), who amazes everybody. SpongeBob wins the science fair and thanks Unikitty. Cindy appears in the lab one more time to ask Unikitty to tell him she said hi, but instead Dr. Fox yells her to leave again.