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 Turner 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 and begins playing 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, 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. Stealing a floating skateboard, Timmy rockets himself across town and crashed into Cindy Vortex who, thinking Timmy is a genius like Jimmy, grows feelings for him.
Meanwhile, Jimmy 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 teleportation pen. Seeing this, Denzel 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, the Decimator game transforms Goddard into a monster and he begins destroying the town. Timmy attempts to stop him but his instead eaten and trapped inside. Cindy uses the frequency of one of Jimmy's laser pens which Timmy mistook for his Auto-Poofer to communicate with him. Cindy guides Timmy to the disk drive and Timmy realizes that removing the game from Goddard would return him to his original programming. With the laser pen out of power, Timmy uses his teeth to bite through the system and saves Goddard. Cindy 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. With Goddard returned to normal, Jimmy makes contact with his friends and informs Timmy that Crocker is in Fairy World.
Crocker escapes from Jimmy and takes a tour, 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. 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. 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.