A race of beings known as Monobails exists in another world, sustaining themselves not by ordinary food but by burning elemental stones in reactors on their bodies. Each Monobail is tied to a specific chemical element from the periodic table; the heavier and rarer the element, the more powerful the Monobail. They were once ruled by the Albatross princesses, who wielded the power of a single, all-powerful holy crystal. That crystal has now shattered, its five isotopes or sacred stones scattered across the world, and the princess has lost her authority.

The story begins on Earth when a junior high school student named Yuuki Shinohara defends a strange, unpopular girl from bullies. Known to her classmates as the Trash Girl for her dirty uniform and habit of scavenging through garbage, the girl is actually the fallen Albatross princess, who goes by the name Sakura Asakura while in human guise. After saving her, one of the scattered holy crystal fragments accidentally embeds itself into Yuukis hand, granting him the power to control fire and heal his battle wounds. This power, however, draws its energy from Sakuras own dwindling strength.

Yuuki, the heir to a martial arts dojo who has been subjected to grueling physical training by his mother since childhood, decides to use his newfound abilities to protect the weak princess, who is too feeble to fight on her own. Sakura initially resists involving a human in the conflicts of the Monobails, who are far stronger than any person, but she ultimately accepts his help. In her true form, Sakura transforms into a winged humanoid with white hair, yet even then she remains extraordinarily weak without the holy crystals power.

Together, they begin searching for the four remaining crystal fragments, encountering various Monobails who have also come to Earth. Their opponents include Kagu, a Titanium Monobail who has infiltrated their school by killing and impersonating a teacher; Nody, a Zinc Monobail; and the powerful elite Monobail named Crane, whose element is antimony. Other notable characters include the gentle giant Lebaio, a Magnesium Monobail, and the combat medic Goose, a Bromine Monobail. As the series progresses, Yuuki discovers that his own father was a human-looking Monobail, making him a half-human hybrid.

The manga builds toward a climactic confrontation with powerful elite Monobails such as Shrike, a Strontium Monobail. The narrative arcs follow the duo as they battle increasingly strong enemies, each fight revealing more about the shattered crystals power and the political turmoil in the Monobail world. The series ultimately concludes after only two of the five sacred stones are collected, leaving the fates of the remaining three isotopes including water and light unresolved, with one fragment in the possession of an ally and the others at unknown locations.