The story takes place in what appears to be a fantasy world (but is in fact this world in the distant future) and revolves around a 15-year-old girl named Pacifica Casull, the sister in a pair of twins born to the royal family of a kingdom called Leinwan who is, literally, thrown away at birth. The 5111th Grendel Prophecy predicts that she will be the "poison that will destroy the world" if she reaches her sixteenth birthday. To prevent this she is dropped off a cliff as an infant ("scrapped"). Believed to be dead, her survival remains no more than a rumour until she is already 15 years old.
Pacifica is rescued by a court wizard and adopted by the commoner Casull family. Her foster siblings, Shannon, a swordsman, and Raquel, a wizard, become her protectors. Both siblings are extremely powerful, and more often than not they easily break out of whatever difficult situation they face.
Her siblings travel with her throughout most of the story, protecting her from the numerous attempts on her life by people who fear the outcome of the prophecy. Both siblings' skills see constant use. By contrast, Pacifica is mostly a typical fifteen-year-old, and her inability to defend herself is a recurring source of self-doubt for her, as is the constantly repeated insistence that she will destroy the world. As the series progresses, the truth about the prophecy slowly comes to light, but even as more of the truth is revealed, more questions arise. Pacifica must discover her hidden destiny, even as powerful beings called Peacemakers, who are worshipped in this world as demi-gods, continually manoeuvre to have her destroyed, and, at the same time, a mysterious being called a Dragoon comes to the assistance of Pacifica and her guardians, offsetting to some extent the attack of the Peacemakers. It turns out that Pacifica is not only not "the poison that will destroy the world" but, in reality, mankind's last hope, and all part of a plan that was set in motion 5000 years before by scientists among the human resistance to aliens during what were called the Genesis Wars.