The game is set in the year 2174, two years after the events of Zone of the Enders. It follows Dingo Egret, a miner working on Callisto. He inadvertently discovers the Orbital Frame, Jehuty, hidden. When he is attacked by BAHRAM forces who have come to seize it, Dingo climbs into Jehuty and engages the attackers, which include a female Orbital Frame runner named Ken Marinaris. During the battle, Dingo enters the BAHRAM battleship, seemingly defeating Nephtis, an Orbital Frame controlled by an AI program based on Viola's fighting style, but is subdued by Anubis, Jehuty's superior counterpart controlled by Col. Ridley "Nohman" Hardiman, leader of BAHRAM. Nohman requests Dingo to join him once again. When Dingo refuses as his comrades were sacrificed by Nohman years ago, Nohman shoots him and leaves him to die.