Agatha and Sophie have returned home and they are accepted as heroes who have returned home. Unfortunately for Agatha, Sophie is taking advantage of this opening. Whereas Agatha wants nothing to do with fame, Sophie puts on many shows. At Sophie's father's wedding, Agatha suddenly wishes for another ending to her story, an ending with Tedros. This wish causes magical arrows to come and messages saying to give Sophie to them. Angry, the town turns into a mob demanding Sophie be given to whoever wants her. The Elders says that they are protecting Sophie, but in reality they are planning to give in to the mob. They tell Sophie to stay in the church alone; and Agatha, thinking that Sophie would be safe, leaves. Sophie is taken into the forest with a message on her chest made from her own blood. She is hung on a tree with the message Take Me and left to die. Agatha finds Sophie and runs away with her trying not to be attacked by the mob. They soon arrive in a fairground and they notice butterflies trying to help them. They get on a train unknowingly bound for the School of Good and Evil.
Arriving at the doors of the School for Good, they are swamped by a herd of girls from both schools robed in blue. As the girls are introduced to their classmates (including a silent girl named Yara) and taken around by the new Dean, Evelyn Sader, they notice that the school has been changed and the fairy tales on the walls have changed as a result, with the damsels in distress now becoming warrior women. Agatha mentions the absence of boys, and it is discovered that after they left, all the girls from the School for Evil were repelled and had to come to the School for Good seeking refuge. The boys from the School for Good were then expelled by an unseen force and had to go to the School for Evil.
As the truth and impact of what they have done settles on the girls, Sophie is horrified to discover that they are back due to Agatha's wish for a different ending to their tale, mainly that she ends up with Tedros. Agatha denies this and insists that all she wants to do is return home. Agatha sneaks into the School for Boys with Sophie following her under an invisible cape to stop her from kissing Tedros. Agatha attempts to speak with Tedros, does, and almost kisses him but in the moment before they do, Tedros becomes paranoid about Sophie still being alive and able to seek revenge and starts raving. As they argue, Sophie hidden underneath a table in the room seizes the opportunity and shoots a spell between them. Agatha thinks Tedros attacked her and Tedros thinks Agatha attacked him and they both start fighting. Agatha then flees convinced Tedros is evil. She goes back to the school for good where Sophie is waiting for her, pretending not to have known a thing. Eventually, it is decided that one of the girls must become a boy to integrate into the School for Boys to steal the Storian. Sophie is chosen and integrates into the boys' school. Soon Sophie's name as a boy is Fillip. Fillip and Tedros have problems at first, but soon, Fillip is protecting Tedros. Then they become the best of friends. Filip confesses to Tedros that he (Sophie) would do anything to see his (her) mother again. Tedros says he wouldn't want to see his, because his dad (King Arthur) sent out a warrant for her head (she had cheated on King Arthur with Sir Lancelot), and when he turns 16, he'd have to honor that warrant.
Then later in the forest at the Trial by Tale Agatha is hiding when Fillip comes with Tedros. Soon, Agatha sees that Tedros leans in to kiss Filip, but Agatha only sees their lips almost touch. She blames "Filip." As the three argue, suddenly, the spell wears off and Filip turns back into Sophie. Tedros is confused and angry, but then, the new "School for Girl" teacher Evelyn Sader, sister of August Sader, has her butterflies fly off trees as they carry the Storian and Evelyn to the trio. The New Dean brings out Sophie and Agatha's fairy tale book and lets the Storian write. Agatha and Tedros kiss because Evelyn made Sophie have symptoms. As the Storian is about to finish writing the end but the dean stops the Storian. Evelyn conjures the School Master's ghost and her butterflies turn red from being blue. Sophie kisses the ghost and as it becomes the School Master, the School Master kills Evelyn and sends Agatha home. The School Master tries to kill Tedros, but just before that happens, Agatha grabs Tedros and takes him with her, and the two schools become a malevolent School for Evil together. For now, as it says, their wishes were granted.