After wishing for a challenging virtual reality game, Timmy goes to the bathroom and leaves it unattended, and Chester and AJ decide to play. Realizing what has happened, Timmy must go into the game and play to save them.

While watching Crash Nebula, Timmy wishes for an alien to play with. So, Cosmo and Wanda take a real alien prince - Mark. His parents are furious and travel to Earth to blow it up. In the meantime, Mark has fallen in love with Vicky, and Timmy can't wish him away because GodParents can't interfere with true love. Timmy goes to Mark's parents and asks them to convince their son to forget about Vicky, but Timmy must first pass their toughest tests. Will he be able to fix this mess and save the Earth from destruction?

After Timmy brings an extinct dinosaur to school, his crazy teacher suspects that he has Fairy GodParents, so he tells Timmy he wants to have a conference with his "parents." Since he has aspirations of "a new world order," he thinks that if he catches fairies, he can harness their power and rule the Earth. Timmy knows he can't explain to his real parents how he managed to come across an extinct dinosaur, so Cosmo and Wanda pose as his parents.

Timmy has a giant crush on Trixie Tang, the most popular girl in school, but she doesn't even know he exists. In order to get Trixie to notice him, Timmy wishes for a long list of superficial things to make him popular.

Cosmo and Wanda shrink Timmy so he can complete his assignment on the microscopic universe but problems ensue when Cosmo and Wanda, who have also shrunk themselves, get eaten by Vicky. Timmy must now go inside Vicky to save his godparents but stirs up a lot of trouble in the process. To make matters worse, Vicky plans on tearing apart the house and blaming it all on Timmy to his parents.

When Timmy breaks his dad's sentimental, grade school trophy and gets punished, he wishes himself back in time to stop his dad (as a kid) from ever winning the dumb thing in the first place.

After Wanda gets mad at Cosmo on their umpteenth anniversary, Cosmo visits Fairy World. There, his mom, who has always hated Wanda, announces that she has found him two new girlfriends, Twinkle and Star. In order to get Cosmo back, Wanda must compete against Twinkle and Star in a game show hosted by Cupid, but Cosmo's mom will do anything to ensure that he doesn't go home with Wanda.

Timmy meets his favorite superhero, The Crimson Chin, but the discovery that he is fictional sends the hero into a deep depression. Timmy must now reverse this situation, and as a result, he gains the superhero alter-ego of Cleft the Boy Chin Wonder.

Timmy switches lives with Vicky's dog, but swiftly discovers that the dog actually has it just as badly as he does.

When Timmy feels sorry for the town's caged, prize goat, Chompy, and wishes he could be free, the goat disappears and Vicky gets blamed for goat-napping.

Timmy wishes for everyone in the world to be the same when an evil dentist won't give him his ball back. Problems inevitably ensue, and Timmy can't wish things back to normal as Cosmo and Wanda aren't able figure out who he is.