After successfully stealing four of the Earth Alliance's prototype Gundam mobile suits, ZAFT reverse engineers them and incorporates new technologies such as Phase Shift armor and beam sabers into their own mobile suits. With these new technologies, ZAFT also builds several Gundams of their own under the direction of leader Patrick Zala. Unlike previous Gundam designs, these new units feature a dangerous new technology: the N-Jammer Canceler. ZAFT originally develops the N-Jammer to prevent the Alliance from using nuclear weapons, but this also means that mobile suits have to be powered by short life energy batteries. By creating the N-Jammer Canceler, a mobile suit can use a nuclear fission reactor and function for a nearly unlimited amount of time even with Phase Shift armor activated. Unfortunately, the N-Jammer Canceler technology proves to be a Pandora's Box that falls into the wrong hands.

The ZGMF-X09A Justice Gundam is one of the new Gundams built by ZAFT. The main feature of this mobile suit is the Fatum-00 backpack which also doubles as a subflight system operable in space or on Earth. The Fatum-00 can also be operated via remote control and be used as a separate attack unit in battle. The Justice Gundam's main armaments are stored on the backpack, but a pair of vulcan guns, beam sabers and beam boomerangs are located on the main body. Armaments on the backpack include various machine guns and a pair of beam cannons for use in HiMAT (High Mobility Aerial Tactics) mode. In addition to these armaments, the Justice Gundam is capable of using something far more powerful: the METEOR support system. This mobile weapons platform is designed specifically for use by the Justice Gundam and ZGMF-X10A Freedom Gundam and is stored aboard the support ship Eternal. By using the METEOR, the Justice Gundam can deliver a blitzkrieg attack utilizing various cannons, missile launchers and with two long beam swords.

The Justice Gundam is deployed in late C.E. 71 by Athrun Zala under orders from his father Patrick to locate or destroy the stolen Freedom Gundam. However, after locating the Freedom Gundam, Athrun decides to switch sides and join his old friend and former enemy Kira Yamato. Athrun joins the battle against the Alliance at Orb, and after the collapse of the neutral nation he goes into space with the Archangel and the Orb ship Kusanagi. There, Athrun is joined by Lacus Clyne and her supporters, who steal the support ship Eternal and its two METEOR units. With the powerful METEOR support system, Athrun is able to prevent the PLANTs from being destroyed by nuclear missiles and also destroy the GAT-X131 Calamity Gundam. At the war's end, Athrun self-detonates the Justice Gundam within the massive laser cannon GENESIS to destroy it, but he is rescued by Cagalli Yula Athha's MBF-02+AQM/E-X-01 Aile Strike Rouge.