Zone of the Enders: The game takes place in the year 2172; mankind has colonized Earth's, Mars', and Jupiter's moons. A military force known as BAHRAM sends its primary offensive unit to attack Antilia, a Jupiter colony, in an attempt to secure two advanced machines known as Orbital Frames. One of the few colony survivors, a young boy named Leo Stenbuck, witnesses a falling Laborious Extra-Orbital Vehicle (LEV) killing his friends. He flees to a hangar, where he finds an Orbital Frame by the name of Jehuty. Using this suit and its built-in intelligence, A.D.A, he fends off the BAHRAM forces led by officer Viola who seek to claim Jehuty on the orders of their leader, Nohman. Leo is then contacted by Elena Weinberg, the commander of the civilian transport vessel Atlantis; it belongs to Earth's military forces, the United Nations Space Force. As Jehuty's original pilot died during the attack, Elena requests Leo's assistance to deliver Jehuty back to them so they can take it to Mars. Leo, however, refuses to kill enemies.

Zone of the Enders: 2nd Runner: 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.[6] 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.