Timmy Turner and Jimmy Neutron become bored with their very easily outmatched competition, so they team up and create a villain to fight. Their villain won't be evil and refuses to destroy him. Eventually, he does in turn attack Retroville from feeling neglected after Timmy and Jimmy abandoned him. Jimmy fights back with a J tank but their villain then adapts to stop it because Timmy wrote adaptable as one of its powers instead of adoptable. Then the villain attacks Dimmsdale and rids all of the fairies of their power and steals Jimmy's intelligence! Then, their new villain known as Shirley is attacking them nonstop. They then trick Shirley into going into Retroville to search for Jimmy and Timmy, but soon after they find Shirley putting citizens of both worlds into his own, alternative world like where he was born in.

Shirley now has taken over both worlds and is planning his revenge against Timmy and Jimmy for abandoning him like that.

When Mr. Crocker falls off the classroom, Timmy wishes he had a new permanent teacher named Mrs. Sunshine, but she turns out to be an evil fairy-hunter as Mrs. Doombringer. Timmy must protect his fairies from the evil teacher and get Mr. Crocker back.