A chaotic duel with characters from The Fairly OddParents and Jimmy Neutron erupts 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.
Timmy hasn't done his science project, so he wishes he was in the greatest laboratory in Dimmsdale and thus ends up in A.J.'s lab. Using an Auto-Poofer given to him by Cosmo and Wanda, he goes back to his own room. He wishes he was in the greatest lab in the multiverse. Timmy, now in CGI, arrives in Retroville in Jimmy's lab. Jimmy can be seen currently is updating Goddard when Timmy drops in and starts to mess with his inventions. Jimmy accidentally uses Timmy's Auto-Poofer, causing him to disappear toDimmsdale. 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, Carl and Sheen drop by and mistake Timmy for Jimmy due to Sheen believing Jimmy has shrunk his own head. After playing with some of the experiments, Timmy bumps into Cindy who falls in love with Timmy, believing him to be more handsome and smarter than Jimmy.
Back in Dimmsdale, Jimmy, now in 2-D, finds himself in Timmy's room and meets Cosmo and Wanda, who (for their sake) he believes to be holographic computer fairies. However, Timmy's Dad, Vicky, and several kids in Timmy's school believe Jimmy to be Timmy using a costume to make up for not doing his science project. Jimmy inadvertently uses the Auto-Poofer in front of Mr. Crocker who realizes that he has found a way to get into Fairy World. Jimmy ends up back in Timmy's room and after finding it only teleports him there, combines it with Timmy's handheld video game so he can teleport anywhere. After tracking Jimmy to Timmy's home, Mr. Crocker steals Jimmy's device that would get him to Retroville, and teleports him, Jimmy, Cosmo and Wanda to Fairy World.
Back in Retroville, Timmy and Cindy enjoy hanging out with each other at the Candy Bar, but Goddard 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. Timmy realizes what he has done, but before he can escape, he is eaten by the Decimator. With time running out for Timmy, with Cindy's help, manages to shut down Goddard, and restore him to normal. Fortunately for Timmy, Cindy stupidly believes that Timmy created the evil Goddard so that she could solve the entire incident.
In Fairy World, Jimmy comes in contact with Timmy, who is alarmed to find out that Mr. Crocker is in Fairy World. Jimmy does not listen to Timmy's plan to get Crocker out of Fairy World and refuses to help him. Crocker then discovers that if he stole magical equipment and knocked down the Big Wand (which powers the fairies' magic); the fairies would surrender to him. Crocker steals a suit of magical equipment and knocks down the Big Wand, making all of the fairies, including Cosmo, Wanda and Jorgen von Strangle powerless. Jimmy then gets ready to leave after stealing the Auto-Poofer from Crocker. After talking with Timmy, who convinces Jimmy that Cosmo and Wanda are as real to Timmy as Goddard is to him, Jimmy makes his Brain Blast and has plan to stop Crocker. Using a 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. 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 her’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 Timmy reminds them that he still hasn't finished his science project. Out of a wormhole appears Goddard, now in a 2-D/CGI form, which amazes everybody. Timmy wins the science fair and thanks Jimmy. Cindy appears in the lab one more time to ask Jimmy to tell him she said hi, but instead Jimmy yells her to leave again.
- Ash Ketchum, Pikachu, Misty, Brock, Serena and the Sailor Scouts, Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, D-Team, Alpha Gang, The Dazzlings, Dr. Facilier, The Grand Duke of Owls, Oogie Boogie, Kurumi Tokisaki, Attila and Hun, The Crime Empire (Joker, Harley Quinn, Penguin, Two-Face, Negaduck, Quackerjack, Megavolt, Bushroot, and The Liquidator), Kyoko Kudo, Yuki Kashiwazaki, Aya Kanazawa, Spectral Space Pirates, and Team Rocket guest stars in this film.
- The stroyline will contiued in Weekenders and Jimmy/Timmy Power Hour 2: When Nerds Collide!.