"Scrapped Princess" is a fantasy manga series set in a world where magic and technology coexist. The story centers on Pacifica Casull, a 15-year-old girl prophesied to bring about the destruction of the world on her 16th birthday. Labeled as the "Poison that will kill the world," she is marked for death by the ruling religious order, the Peacemakers, who seek to eliminate her to prevent the prophecy's fulfillment. Pacifica is rescued as an infant by the Casull family, who raise her as their own, and she grows up unaware of her fate.

Pacifica's adoptive siblings, Shannon and Raquel Casull, vow to protect her from those who seek her death. Shannon, a skilled swordsman, and Raquel, a powerful sorceress, accompany Pacifica on a perilous journey as they flee from relentless pursuers, including the Peacemakers and other factions that believe in the prophecy. The trio faces numerous challenges, including battles with assassins, encounters with mythical creatures, and the unraveling of secrets about the world's true nature.

As the story progresses, it becomes clear that the world is not what it seems. The setting is revealed to be a post-apocalyptic Earth, where advanced technology has been misinterpreted as magic by its inhabitants. The Peacemakers, who enforce the prophecy, are actually an artificial intelligence system designed to maintain order after a catastrophic war. Pacifica's existence threatens this system, as she is a key to unlocking humanity's suppressed memories and restoring their understanding of the world's history.

The narrative explores themes of destiny, free will, and the clash between technology and tradition. Pacifica's journey forces her to confront her role in the prophecy and the moral implications of her survival. The series balances action, mystery, and emotional depth, with the bond between Pacifica and her siblings serving as a central emotional anchor. The story culminates in a confrontation that challenges the very foundations of the world and the characters' understanding of their place within it.