Crocker has fallen into a well and so Timmy's class has been assigned a substitute teacher called Mrs. Sunshine and she seems very-very nice until Timmy wishes for her to be his permanent teacher, she turns out to be even worse than Mr. Crocker when she is really an expert fairy hunter named Mrs. Doombringer.
Timmy hasn’t studied for a test in Mr. Crocker’s class, so he wishes for a magical device that allows him to change places with anyone who comes in contact with it. Cosmo and Wanda are in a hurry, so they give Timmy his wish. At school, he uses this device to change places with AJ, but after that, his plan backfires. Will Timmy be able to stop Crocker from finding out about Timmy's fairies? Find out.
Timmy is at the beach and he’s bored silly. He, Cosmo, and Wanda set off to explore the deep, and everywhere they go, but Cosmo seems to be hated by every single fish. Soon, they end up in the lost city of Atlantis. Timmy appeals to Atlantis’ leader, King Greg -- if he can show good cause why Atlanteans should be happy beneath the sea, Cosmo will be set free. Will Timmy save Cosmo?
Remy Buxaplenty has come home from military school for spring break. All he can talk about is how great his new school is, making Timmy, Chester, and AJ very jealous in the process. Timmy decides they should all get to go to Remy’s fancy academy and wishes for three scholarships. Once the boys get to their new school, they find that it is not quite the paradise Remy described -- it’s the exact opposite. The students have to get up before dawn every morning, all the teachers are drill sergeants, and pets are strictly forbidden which means that Timmy’s pet goldfish (a.k.a. Cosmo and Wanda) are confiscated and placed in storage. This of course was Remy’s plan all along, and now that Timmy can’t get to his God Parents, he cannot wish himself out of this nightmare.
Dad keeps trying to help Timmy with his homework. But he’s not the brightest dad, so any help he gives does more harm than good. How can Timmy get his dad to stop helping without hurting his feelings? He doesn’t. He completely avoids the subject by wishing that his dad was smart. Now that Dad has the brains of a genius, he home-school’s Timmy and pays a lot more attention to things like Timmy’s goldfish. In all the years that Timmy has had his pet fish, not once has he fed them. Dad concludes that they must be a new breed and sets out to dissect the fish in front of the entire scientific community.
Timmy's reading a find-it book when Mark Chang, in his traditional alien form, shows up. His changer is broken, and without it, Mandie will find him. In a last ditch effort to save Mark, Timmy wishes the school was like his book. But she is about to turn the school into a crater if Mark doesn’t show himself. If Cosmo and Wanda had their wands, Timmy could just wish her away. But where are the wands hiding?
Cosmo's Fagiggligland (what fairies use to transform into diffrent things) isn't working and might loose his job being Timmy's godparent. The gang must get Anti-Cosmo out of Anti-fairy jail in order to do a transplant performed by Dr. Rip Studwell. But Jorgen Vonstrangle won't let them through or let Anti-Cosmo out!