Once again, Timmy Turner's mother and father have gone on a vacation, and left Timmy with the evil babysitter Vicky. When Timmy tries to make a wish, his fairy godparents Cosmo and Wanda tell him that it's against "Da Rules". Outraged, Timmy wishes he didn't have to follow the rules. As a result, Cosmo destroys the book; when Vicky arrives, she gains possession of Da Rules. She wishes that Timmy was still sleeping, and since she has possession of a fairy item, her wish is granted. Timmy, Cosmo and Wanda go to Fairy Court, and are accused of destroying Da Rules. Jorgen gives the three of them 49½ hours to find the missing pages of Da Rules. Timmy must navigate through ten levels and find the pages before Vicky's wishing goes too far. By the end of the game, everything is back to normal and Da Rules has all of its pages back.
The PC version features a different plot. In this version, Juandissimo Magnifico tricks Timmy into wishing the book destroyed so that Cosmo and Wanda will get in trouble for it. It also notably features an appearance by Vicky and Tootie's mother (at Timmy's age, as the level featuring her is set in the past), named Nicky. Here, she is shown behaving a lot like Tootie, and Timmy initially mistakes her for Tootie when he first sees her, although the in-game graphics depict her as resembling a young Vicky.
In the Game Boy version, Anti-Cosmo arrives to steal the book, and Vicky is defeated at the very end to restore peace.