Before Jimmy Neutron could get back home to Retroville using Timmy's Auto-Poofer mixed with his Gamebubby, Denzel Crocker breaks into Timmy's room and snatches it out of Jimmy's hand and changes the location from Retroville to Fairy World and teleports himself, Jimmy and Cosmo and Wanda there.
As soon as they were in Fairy World, Crocker starts to cause trouble. He steals supplies from the Fairy Armory and knocks down The Big Wand cutting off all the fairies supply of magic. All the fairies including Cosmo, Wanda and Jorgen Von Strangle become powerless and Crocker takes over Fairy World, turning Jorgen into as dog, changing a street sign to his name, changing the sign to Crocker World and a bunch of mountains into giant statues of himself.
Jimmy was able though to get the teleportation device back from Crocker but using Cosmo's crown to make an electromagnetic field. Jimmy was at first going to leave them with Crocker becoming the fairies' new king, but when Timmy explains how much his fairies mean to him as much as Goddard does to Jimmy he decides to stop him.
Jimmy built a robot suit out of many of the science fair projects for Cosmo and Wanda to use to distract Crocker while Jimmy fixed The Big Wand. After connecting the wires and plugging The Big Wand in, the fairies power is restored and all the fairies have their powers again and Fairy World is restored back to normal.
Jimmy then defeats Crocker by zapping him with Jorgen's wand turning him into scientific objects and Jorgen in dog form erases Crocker's memories by attacking him. Timmy then wishes he and Jimmy were back in there own home towns and Cosmo and Wanda magically teleport Jimmy and Timmy back to each others home dimensions.