In the year T.C. 4767, humanity has been displaced from its birthplace, Earth, for four millennia. Facing the hostile alien entity known as the Gnosis, mankind urgently seeks ways to survive. One such effort is the creation of KOS‑MOS, a highly capable android engineered by Vector engineer Shion Uzuki. When their ship is destroyed by the Gnosis, Shion and her companions are thrust into a conflict with no clear sides.