A chaotic duel with characters from The Fairly OddParents and Jimmy Neutronerupts when Timmy wishes to go to the greatest lab in the universe for his science fair. The greatest lab in the universe just happens to be in Retroville, Jimmy Neutron's lab, but Jimmy accidentally teleports himself into Timmy's universe. Now the two are stranded in each other's worlds. Now Timmy must shut down Goddard, who Timmy uploaded a destructive video game into, before he destroys Retroville. Meanwhile, Jimmy must stop Mr. Crocker from taking over Fairy World.
Realizing he is unprepared for his science project, Timmy wishes he was in the greatest lab in Dimmsdale, but he ends up in A.J.'s lab, and he can't just use A.J.'s lab because he'll suspect that Timmy used his technology.
Taking with him a magical Auto-Poofer that poofs him back to his bedroom, he wishes himself to the greatest lab in the universe, and is transported to the lab of Jimmy Neutron in the city of Retroville. Timmy (now CGI animated) begins fiddling with the inventions stored there. Jimmy confronts him and accidentally activates the Auto-Poofer and sends himself to Dimmsdale.
Exploring the lab, Timmy finds Jimmy's robotic dog Goddard in the middle of an automatic tune-up and, mistaking him for a video game system, and foolishly downloads the video game Decimator into Goddard's hard drive.
Timmy meets Jimmy's friends Carl and Sheen and the two use the absent Jimmy to play with his unguarded inventions. Jimmy's mother, Judy arrives and thinks Timmy is Jimmy and grounds him when Timmy talks back. Timmy then using Jimmy's hypnotizing device to think she is Mighty Mom.
Stealing a rocket-powered skateboard, Timmy rockets himself across town and crashed into Cindy Vortex who, thinking Timmy is a genius like Jimmy, falls for him. The two then go to try out all of Jimmy's inventions.
Meanwhile, the Decimator video game finishes downloading and transforms Goddard into the title character. Goddard escapes the lab and starts chasing after Jimmy's dad, Hugh.
Meanwhile, Jimmy (now in regular animation) meets Cosmo and Wanda and believes they are holographic super computers. The town mistakes Jimmy for a Timmy since Timmy's used outlandish disguises to escape responsibilities. Jimmy goes to Dimmsdale Elementary School and brags of Timmy's Auto-Poofer as a scientific teleporting pen. Seeing this, Mr. Crocker recognizes it as a magical item and chases Jimmy back to Timmy's room. Realizing the Auto-Poofer's limitations, Jimmy combines it with a Game Buddy and invents a true teleportation device that can take him back to Retroville. But before Jimmy can use it, Crocker steals it and uses it to transport to Fairy World.
Back in Retroville, Cindy and Timmy are at the Candy Bar, Cindy is still oblivious to the fact that Timmy's not a genius. Just then, Carl, Sheen, and Libby try to warn Timmy and Cindy that Goddard's been transformed into a monster. They show them what's going on, but Timmy and Cindy don't listen and proceed to finish their date. Carl, Sheen, and Libby then decide to stop Goddard themselves. But, they are unsuccessful and Goddard becomes ginormous and chases after the kids.
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 now sees that the game is getting out of control. He tries to get home to Cosmo and Wanda for help. but is instead eaten and trapped inside of Goddard. Cindy decides to help Timmy by uses the frequency of one of Jimmy's laser pens which Timmy mistook for his Auto-Poofer to communicate with him. Cindy tells him to get to Goddard's central core to deactivate him.
Back outside, 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.
Cindy guides Timmy to the disk drive and he arrives, just as Goddard is about to destroy the town with his rockets. However, the laser pen runs out of power, so Timmy uses his teeth to bite through the system and shuts the game down, causing Goddard to deactivate and the town is saved.
Cindy arrives in Jimmy's hover-craft and confesses to Timmy that she believes he created the disaster on purpose just to allow her the opportunity to resolve it and she kisses him, much to the other's disgust. Just then, Goddard shrinks and returns to normal. With Goddard back to normal, Jimmy makes contact with his friends and informs Timmy that Crocker is in Fairy World.
While Jimmy and Timmy have an argument, Crocker escapes from Jimmy and takes a tour (by disguising himself as an imp), learning that the Fairy Armory houses a number of magical weapons which Crocker poofs into and steals. Powered by magic, Crocker destroys The Big Wand and leaves the fairies powerless and turns Jorgen into a dog. Thinking the fairies to be unreal, Jimmy retrieves the teleporter from Crocker and nearly leaves the fairies behind. But Timmy uses Goddard to help Jimmy understand what the fairies mean to him and Jimmy decided to stay and fight for them. Returning to the school, Jimmy combines the science fair entries into a robot which Cosmo and Wanda use to distract Crocker while Jimmy uses the armory to return power to the Big Wand. Crocker is also drained of his armory and Jorgen erases Crocker's memory by attacking him.
With the fairies' magic restored, Timmy wishes the two were returned to their home town and the two shake hands and make amends. Cindy tells Timmy she'll never forget him, but Jimmy tells her to get out of his lab.
Back home, Timmy realizes he still never found time to finish his science fair project. On the verge of being disqualified, Jimmy perfects the teleporter and sends Goddard to Dimmsdale. Timmy wins the science fair and thanks Jimmy for his help. Cindy notices Timmy is on the screen and wants to talk to him, but Jimmy yells at her to get out of his lab.