The Republic of San Magnolia has been at war with the Empire of Giad for nine years. Though it initially suffered devastating losses to the Empire's autonomous mechanized Legions, The Republic has since developed its own autonomous units, called Juggernauts, which are directed remotely by a Handler. While on the surface the public believes the war is being fought between machines, in reality, the Juggernauts are being piloted by humans, all of whom are "86"—the designation given to the Colorata minority of San Magnolia. The 86 originally had equal rights, but were persecuted and scapegoated by the dominant Alba race and the Alba-supremacist Republic government to the point where Colorata were both officially designated and popularly considered subhuman. The 86 were not permitted to have personal names and were immured in internment camps in the 86th District (their namesake); all the while being forced to fight in the Republic's war with the Empire to receive better treatment.

Major Vladilena "Lena" Milizé, an Alba noble and military officer in the San Magnolian military, is an outspoken activist against the grave mistreatment of the nation's Colorata minority, and the willful deception of the Republic government to the general public. She is assigned as the Handler of the Spearhead Squadron of the Eastern Front: an elite unit composed entirely of 86 veterans who have earned names. Led by their squad leader, Shinei "The Undertaker" Nouzen, the Spearhead Squadron is infamous among military officials. Its notoriety stems from the state in which its commanding officers are left: Handlers presiding over the squad have descended into insanity and some have gone as far as committing suicide. Lena, an avowed 86 sympathizer, gets to know the Spearhead Squadron in her time as head of the contingent. At same time, Lena and Shinei learn a dark secret: the Republic and the war with the Empire are not what they seem.