Long ago, twin brothers Rhian and Rafal founded the School for Good and Evil, created to groom fairy tale heroes (called “Evers”) and villains (called “Nevers”) respectively. Dissatisfied with evil’s constant submission to good, Rafal attacks Rhian using blood magic. Defending himself, Rhian throws Rafal off a cliff, presumably killing him.

Years later, in the village of Gavaldon, best friends Sophie and Agatha learn about the legendary school from the bookshop owner. While the cynical, misfit Agatha is skeptical, fairy tale-obsessed Sophie leaves a letter for the School at a tree, hoping to escape ordinary village life and become a princess. A few nights later, Sophie attempts to run away from Gavaldon in secret. When Agatha finds out and tries to intervene, a giant stymph suddenly snatches up both, flying them to the School. To their dismay, however, Agatha is dropped at the School for Good while Sophie is delivered to the School for Evil. Agatha protests, wishing to return to Gavaldon, while Sophie wants to transfer to the School for Good. At the welcoming ceremony, Agatha and Sophie meet Tedros, the son of King Arthur and the most popular Ever prince. In the library, Rafal manifests to Agatha, warning her to stay away from Sophie. Agatha reunites with Sophie and they seek out School Master Rhian and the magical Storian pen. Rhian informs Sophie he'll only allow her to switch schools if she can prove herself an Ever by attaining true love's kiss. Sophie casts Tedros as her true love and enlists Agatha’s help.

Meanwhile, Agatha and Sophie struggle in their respective classes and are outcast by their peers. Agatha witnesses as another student, Gregor, is punished for repeated failure and transformed into a stymph. Though Agatha tries to help him, Tedros leaps in to defend her and unknowingly kills Gregor with Excalibur. When Agatha lashes out and insists she does not belong at the School, Ever Dean Clarissa Dovey argues her selfless, empathetic personality makes her the first true princess in a long time. Meanwhile, Sophie gets into an argument and is attacked by Hester, another student, causing Rafal to intervene as a wasp swarm. Never Dean Leonora Lesso interprets this as Sophie's unique potential for finally winning a victory for Evil, something thought impossible for centuries.

When Sophie tries to get close to Tedros, Lesso cuts her hair to break her spirit. Under Rafal’s influence, Sophie undergoes a radical change in both appearance and personality; gaining the favor of the Nevers, befriending Hester and her friends (who become her circle of followers) and rising to the unofficial position of leader of the School for Evil's student body. Though she diverges from Agatha, the latter still tries to aid Sophie by using magic to bring her and Tedros together. An Ever and a Never being together causes chaos between both schools; Rhian determines a “Trial by Tale” to settle the issue. At the Trial, Sophie ends up proving inept in defending herself and Tedros, prompting an infiltrating Agatha to save him in her stead. This results in Tedros ultimately rejecting Sophie for choosing self-preservation over him, with the prince starting a relationship with Agatha.

Convinced by Rafal that Agatha is her enemy, Sophie accepts his offer of blood magic. Sophie incapacitates Dovey, Lesso, and the other school staff, and crashes the Evers’