Timmy, Cosmo, and Wanda find that Fairy World has been taken over by Pixies. Timmy and his fairies must now find a way to get the fairies to own Fairy World again. Pixies charge over to Fairy World changing the fairies into Pixies and changing Cosmo into a manager of a stupid job.
Timmy needs to create a new miniature golf course for his school project (he actually had no project, but his principal's bad guessing led to this). Timmy does not realise that he could simply wish for a the course to be fixed until Wanda blurts it out, however, the wish is not granted. A special addition of the Wand Street Journal reveal that Fairy World has been bought out by the pixies. Timmy goes to fairy world to find out more.
Once they get there, everything is warped into a business oriented city called "Pixies Inc". The recent change causes all the fairies to panic. Timmy goes to Jorgen and finds out that the Pixies bought Fairy World in a hostile takeover, meaning they also bought Fairy Godparents. Pixies treat magic like a business, are against being free-spirited, and have horrible taste in hats. All wishes must now be submitted in writing. The change doesn't even allow Jorgen to bully the trio anymore. Timmy, however, is determined to get his miniature golf course fixed. Sanderson hears their complaint, and tells Cosmo they have been waiting for him. Wanda thinks they are going to fire Cosmo, but instead, he is promoted. It turns out the pixies need to make the fairies think they are still important so that they stay in line, by giving a fairy a large title with a good credit. They cannot trust someone who is too intelligent to understand their motives, so they give Cosmo the line of Vice president (actually rice president). They even make Jorgen work as his assistant. Fortunately for Jorgen, Cosmo is too stupid to get revenge for his centuries of tirment from Jorgen, meanwhile Jorgen attempts to be free spirited despite being under the pixies rule.
Timmy is left with no other choice but to submit hit wish in writing and do the best he can otherwise. Wanda returns and tells Timmy that his wish has been rejected for being too much fun. Cosmo tells Timmy that the Head Pixie loves golf. Timmy takes advantage and manipulates Cosmo into granting his wish and making the Head Pixie come over for a round of golf, in a way of sucking up to his boss. The course is transformed and the Pixies come to play.
Timmy and Head Pixie make the game a little more interesting by betting on the game; If Timmy wins, he gets one free wish, voided by rules entirely, but if Head pixie wins, he gets Cosmo and Wanda, and can use them to do the least fun things possible. Head Pixie continuessly cheats, but Timmy is very skilled at mini golf and succeeds at every course. When Timmy realises that if he screws up on his last course, he will be ruined. Cosmo rebels and cheats for Timmy. Despite this, Head Pixie wins, and Head Pixie fires him, but fortunately, Jorgen's free-spiritedness knocks the ball out of the hole, causing Timmy to win. Timmy wishes that the Fairies ruled fairy world now and forever.
Timmy's teachers enjoy the miniature golf course, as Timmy decided to stick with the one he made himself. Although Wanda is proud of Timmy, Timmy starts to regret it when the course proves to be dangerous. Jorgen punishes the Pixies by using them as darts for his dart board, taking advantages of their pointy heads.