In the Republic of San Magnolia, the ruling Alba majority has declared war with the neighboring Giadian Empire to be a bloodless conflict fought by unmanned drones. This is a lie. The drones are piloted by the Eighty-Six, a persecuted minority group forced to fight and die in the segregated 86th district. The 86 are considered subhuman, stripped of their names and rights, and sent to battle against the Legion, an unfeeling army of autonomous war machines originally created by the Empire.

86—EIGHTY-SIX Alter is a collection of side stories that do not advance the main war plot but instead explore the quieter, more personal moments between battles. These stories are compiled from previously uncollected or unpublished short pieces, offering glimpses into the daily lives and inner worlds of the series central characters, including the Spearhead squadrons reaper, Shinei Nouzen, and their former Handler, Vladilena Lena Milizé. The tone shifts between melancholic, sweet, and humorously absurd, focusing on character interactions rather than strategic conflict.

The main narrative follows two central figures. Shinei Nouzen, known as the Undertaker, is the stoic and battle-weary field commander of the Spearhead Squadron, possessing the ability to hear the thoughts of the dead within the Legion, including his own brother. Vladilena Milizé is an idealistic Alba major who serves as their Handler, communicating remotely from safety. She is one of the few Alba who sees the 86 as human, and she fights against her own militarys racist bureaucracy to improve their grim fates. The Alter stories allow these characters, alongside other squadron members like the hot-headed Theo, the cheerful Kurena, and the mysterious Frederica Rosenfort, to interact as teenagers rather than soldiers.

The narrative arcs in Alter.1, titled The Reapers Occasional Adolescence, are structured chronologically across the main series timeline. The first section focuses on the Spearhead Squadrons time in the Republic of San Magnolia, depicting their life in the internment camps and the rare moments of camaraderie before their desperate escape. The second section follows the squad after their rescue by the Giadian Federacy, showing their difficult adjustment to a society that does not immediately see them as expendable. Later stories take place during the Federacys campaign, including moments in the frigid United Kingdom of Roa Gracia. The collection culminates in a completely non-canonical, fourth-wall breaking short story featuring a chaotic paintball battle royale where all characters, living and dead, compete in a parody of the psychological deduction game Among Us, relying on absurd tactics like identifying perfumes to win.