Two years after the events of Zone of the Enders, former BAHRAM pilot Dingo Egret is mining for ice on Callisto, one of the moons of Jupiter. When he detects indications of Metatron, Dingo investigates, discovering a container with Orbital Frame Jehuty hidden inside of it. The military force BAHRAM, after the frame, launches an attack on Callisto -- leaving Dingo with no other option but to use Jehuty to fight off the attacking BAHRAM forces.

The battle leads Dingo and Jehuty inside a massive BAHRAM battleship, where Jehuty is subdued by its much more advanced twin frame, Anubis. Running Anubis is Nohman, Dingo's former commander, and the man responsible for the death of Dingo's comrades.

The situation on Mars has changed drastically since the events that took place during the Antilia raid. BAHRAM's war potential has increased dramatically, with the Space Force virtually powerless against the threat. Siding with the Space Force while unaware of ADA's mission to self-destruct Jehuty at the core of Aumaan, Dingo, using Jehuty, sets out to take down BAHRAM and their base of operations.