Seven hundred years after the Great War claimed half of humanity, the powerful Gundams that ended the conflict have been declared enemies of peace. In the twenty years since the war's conclusion, these god-like machines have been systematically rounded up and melted down. The evolved humans known as Newtypes, who piloted them, suffered an even crueler fate: they were banished to the space colony Cocytus, which was then gassed, killing its ten million inhabitants before being ejected from Earth's orbit.

Unknown to the Earth government, some of Cocytus's inhabitants survived the gassing. Their descendants built a new civilization within the drifting colony, forming rival city-states including the Imperial City of Gun Dorado, the Desert City of Mu Fasa, and the Icy City of Da Ria. Two years ago, a distress signal from Cocytus was detected, and the colony altered course back toward the Earth Sphere. A survey team of convicts was dispatched to investigate.

The story follows Shagi "Bloody" Kaoris, an infamous assassin and a Neos, a superhuman being descended from Newtypes with powerful regenerative abilities that make her nearly immortal. After being captured and sentenced to public execution in Gun Dorado, Kaoris survives the flames, kills two members of the royal family, and escapes. In the wilderness, she encounters the Earth survey team but leaves them be, mistaking them for agents of a rival city-state.

Kaoris is hired by a Gun Dorado noble to kill Duran Lotus, a former military officer turned assassin who may be her father. Both are Neos, and as they develop a rapport, Duran regains his memories and reveals the truth. His wife Miranda was a royal who conceived Kaoris with another Neos to breed a more powerful pilot capable of activating the Gundam Minerva, the "god" hidden beneath the palace. Enraged, Duran helped raze the palace, resulting in Miranda's death. Duran sacrifices himself to save Kaoris from a hitman.

The narrative expands as three Neos pilots emerge across Cocytus. In Gun Dorado, Kaoris finally claims Gundam Minerva, the machine in whose cockpit she was born while her mother burned alive. In Da Ria, the priestess Lady Jane pilots Gundam Dis. In Mu Fasa, Princess Marinan, imprisoned since accidentally massacring her own people at age seven, pilots Gundam Anubis and takes revenge on her parents for abandoning her. Meanwhile, Master Parna schemes against June, a nun who secretly uses ice barrier abilities for assassinations before performing penance.

Key narrative arcs include the initial encounter between Kaoris and the Earth survey team, Duran's tragic confession and sacrifice, Marinan's awakening and bloody reunion with her family, the gathering of Gundam pilots in Da Ria, and June's confrontation with Master Parna's schemes. The manga follows Kaoris as she uncovers the truth about her origin and the three Gundams, all while navigating betrayals among Cocytus's warring city-states and the looming return of the colony to the Earth Sphere.