Cosmo and Wanda bring Timmy to past times. They meet some of the fairies' former Godchildren. Problems begin when Timmy distracts them and thus alters the future.
Timmy is ashamed of what he did and tries to hide his mistakes until they move to Timmy's era. How will Timmy fix all the changes of the past? How will he defeat the dangerous villainess named "Megan Bacon"?
After Timmy forgets Cosmo and Wanda's 10,000th anniversary of being godparents, he tries to make it up to them by wishing for them to go back in time to meet their previous godkids. First, they meet their first godchild--Erg the caveboy who invented the wheel. Constantly cautious, Wanda warns Cosmo, Timmy, and Sparky not to touch or talk with anyone since even a measly change in the past could completely alter the future. Unfortunately, while Cosmo and Wanda try to stop Sparky from eating a prehistoric squirrel, Timmy walks by Erg and gives him his video game. Seeing the futuristic technology, Erg quickly abandons his work on the wheel and runs off to his cave, now addicted to the handheld console.
Next, Cosmo, Wanda, Timmy, and Sparky go off to see the next child--the Earl of Sandwiches, who is about to invent the sandwich. Once again, Cosmo and Wanda have to go stop Sparky from poofing to the Earl of Nachos, and during their brief absence, Timmy interacts with the Earl of Sandwiches, making him knock over his bottle of milk. After seeing how the bread soaked up the liquid with ease, the Earl of Sandwiches decided to invest his attention to using the bread as a sponge rather than inventing the sandwich.
Afterward, the group moves onto the next child--Benjamin Franklin, who is flying a kite outside in the thunderstorm. Quite predictably, Sparky gets distracted again and Cosmo and Wanda have to stop him, leaving Timmy alone with Ben. Realizing what would happen if he let Benjamin stay out in the thunderstorm, Timmy quickly pushes him out of the way before he would get hit by lightning, and Benjamin Franklin thanks Timmy for helping him realize that electricity was far too dangerous to be meddled or experimented. He then decides to use potatoes to power things instead of hazardous electricity.
Finally, they move onto the last godchild--the evil child Megan Bacon who eventually opened up the Cake 'N' Bacon eatery. Still frightened by her terrible behavior, Cosmo poofs off to hide in the closet, forcing Wanda and Sparky to get him to stop messing around. While they are gone, Timmy is confronted by Megan, who then attacks him with steaming hot, crispy bacon. Later on, however, she opens up to Timmy, telling him that her fairies were making her do homework. Giving some advice, Timmy says that kids shouldn't be oppressed with homework, and he tells her to follow her dreams instead.
After the trip, Cosmo, Wanda, Timmy, and Sparky poof off back to present-day Dimmsdale, only to find it in a huge mess where everything was completely messed up. Cars could not move along smoothly since their wheels were rugged and deformed, the whole town was powered by a giant, mutant potato, and pieces of bread littered the shoddy town. Timmy then realizes that Cosmo and Wanda were gone, and Jorgen informs them that they were fired from being godparents due to the terrible job they did. On the bright side, Sparky was still there and he could also travel through time, so Timmy set out to fix all the messes he made. He takes the video game away from Erg and convinces him to finish the wheel, he stops the Earl of Sandwiches from the crazy bread-sponge idea and shows him how to make a sandwich, and he pushes Ben Franklin back out in the thunderstorm where he gets violently struck by lightning. Strangely, even though he returned Dimmsdale to its regular form, Timmy sees that Cosmo and Wanda were still gone, causing him to come to the realization that he forgot to go back to talk with Megan Bacon, who was now living her dream as a supervillain.
After finding her villainous lair, Timmy discovers that she was planning to burn Fairy World to the ground after encasing it with a butterfly net to disable the fairies from using magic. Timmy recruits Erg, the Earl of Sandwiches, and Benjamin Franklin to help him fight against her, and they are eventually able to save Fairy World. Enraged, Megan Bacon was going to kill Timmy, but she slipped on bacon grease due to her bacon, which also happened to Timmy earlier before the battle. Later on, Cosmo and Wanda poof back to Timmy and he wishes that he never interacted with Megan Bacon and that she would go on to open up the Cake 'N' Bacon.
To celebrate their victory, Cosmo, Wanda, Timmy, Sparky, Erg, the Earl of Sandwiches, and Benjamin Franklin all go to the Cake 'N' Bacon, where Megan Bacon serves them. While ordering their meals, Timmy inquires why nothing changed when he brought Erg, the Earl of Sandwiches, and Benjamin Franklin to the future to fight Megan. However, he is quickly proven incorrect when a giant Mr. Turner appears out the window and he reveals that the Cake 'N' Bacon shop was just a mini model for his set.