Twin brothers Rhian and Rafal established the School for Good and Evil with the aim of cultivating fairy tale heroes, known as "Evers," and villains, referred to as "Nevers." Discontent with the ongoing domination of good over evil, Rafal unleashes a blood magic attack on Rhian, leading to both falling off a cliff, with Rafal seemingly meeting his demise.
Years later, in the quaint village of Gavaldon, best friends Sophie and Agatha learn about the fabled school from the local bookshop owner. While Agatha is doubtful, the fairy tale-obsessed Sophie yearns to escape her mundane existence and become a princess. One fateful night, Sophie attempts to secretly flee Gavaldon, but when Agatha tries to stop her, a gigantic stymph swoops in and carries them both away to the enchanting School for Good and Evil.
To their surprise and dismay, Agatha is unceremoniously dropped at the School for Good, while Sophie finds herself taken to the School for Evil. As Agatha voices her desire to return home, Sophie is adamant that she belongs in Good. The girls seek out School Master Rhian and the magical Storian pen, who informs Sophie that she can only switch schools if she can earn true love's kiss. She pinpoints Prince Tedros, the son of King Arthur, as her true love and enlists Agatha's assistance in her pursuit.
Both girls face struggles in their respective schools, quickly becoming outcasts among their peers. Agatha openly criticizes the superficiality of Good; however, Ever Dean Clarissa Dovey argues that Agatha’s empathy distinguishes her as the first true princess in ages. As events unfold, Rafal reemerges as a swarm of wasps, providing protection for Sophie from another student’s aggression. Never Dean Leonora Lesso perceives Sophie as having a unique potential to achieve a long-sought victory for Evil.
In a bid to get closer to Tedros, Sophie undergoes a drastic transformation—both in appearance and personality—under Rafal’s sinister influence, leading to her rise as an unrecognized leader of Evil’s student body. Despite their growing rift, Agatha persistently attempts to assist Sophie, using magic to forge a connection between her and Tedros.
The union of an Ever and a Never stirs up turmoil within both schools; to resolve the dilemma, Rhian proposes a "Trial by Tale." During this event, Sophie struggles to defend herself and Tedros, prompting an infiltrating Agatha to rescue him, ultimately leading to Tedros rejecting Sophie for prioritizing her own safety over his. Consumed by Rafal’s manipulations into believing Agatha is her adversary, Sophie succumbs to the temptation of blood magic.
Taking drastic action, Sophie incapacitates Dovey, Lesso, and the rest of the faculty, and crashes the Evers' Ball, now transformed into a hag. She threatens Agatha and provokes Tedros into an attack on the School for Evil. This act contravenes the established law that states, "Good defends, Evil attacks," resulting in the two factions magically swapping appearances, igniting an all-out battle.
In her quest for vengeance against Rhian, she discovers he is actually Rafal, who survived the fall, killed Rhian, and has been orchestrating events from within Good to weaken it. He proposes a joint rule with Sophie, declaring her his true love. > As they share a kiss, the Schools begin to collapse, throwing Sophie into despair. Agatha arrives just in time, but Rafal attempts to impale her with the Storian, which had inscribed a predetermined fate. In a moment of heroic sacrifice, Sophie pushes Agatha to safety, taking the blow herself; her choice unravels both Rafal’s spell and the written fate of Agatha, saving everyone involved.
With the help of Tedros and a dying Sophie, Agatha uses Excalibur to vanquish Rafal. Following their victory, Agatha kisses Sophie goodbye, a moment that exemplifies true love, and revives her. The Evers and Nevers come together, leading the school’s staff to merge the two schools into one. As they open a portal back to Gavaldon, Agatha shares a kiss with Tedros before returning to their former lives alongside Sophie. However, a confluence of events pierces the veil between worlds, sending an arrow that prompts Tedros to call out to Agatha, leaving the Storian to proclaim, "this is only the beginning."
