In the year T.C. 4767, humanity has been away from their home planet Earth for four millennia. Their survival is threatened by the hostile Gnosis aliens, and they are frantically searching for ways to defeat them. To fight back, Vector engineer Shion Uzuki created KOS-MOS, a highly advanced android. However, when the Gnosis destroyed their ship, Shion and her companions are left in the midst of a chaotic and unclear battle.