[citation needed] It begins as high fantasy and then quickly mixes into varying degrees of post-apocalyptic and science fiction elements through the application of Clarke's third law.

The story takes place in what appears to be a fantasy world and revolves around a girl named Pacifica Casull, the sister in a pair of twins born to the royal family of a kingdom called Leinwan.

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.

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.

Pacifica must discover her hidden destiny, as powerful beings called Peacemakers, who are worshipped in this world as demi-gods, continually manoeuvre to have her destroyed.

At the same time, a mysterious being called a Dragoon comes to the aid of Pacifica and her guardians, offsetting the attack of the Peacemakers.

Celia was then kept in an area of phase space in a sort of virtual reality for 5000 years, while humanity continued to live on unknowingly in an intangible cage, isolated on a single continent called Dusbin.

For 5000 years, the Peacemakers watched over humanity, keeping cultural development at a standstill, and prepared to wipe out much of the human race if it ever showed any sign of stepping beyond its apportioned limits (as the Kingdom of Leinwan does toward the end of the series when the attempt is made to coerce the Peacemakers into helping them conquer the world).

This causes her to be removed to the phase sphere, where she meets Celia Mauser and is given the choice of whether humanity will remain in their prison or not.

The manga has no plot overlap with the anime adaptation; the only things in common are the three main characters, the idea of the Scrapped Princess, and the Mauser Faith they are running from.

Another three-volume manga adaptation illustrated by Toshinori Sogabe was published from 2016 to 2018 in Famitsu Comic Clear online magazine.