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-X13A Providence Gundam is the final Gundam that ZAFT introduces in the war. One of the new technologies present in the Providence Gundam is the DRAGOON (Disconnected Rapid Armament Group Overlook Operation Network) system. With the DRAGOON system, 11 units are are stored on the Providence Gundam's massive backpack. These 11 units can be controlled wirelessly and attack an opponent from multiple directions. With a total of 43 beam gun nozzles, the Providence can unleash devastating firepower with its all-range attack. However, the DRAGOONs can only be controlled by pilots with a high level of spatial awareness. In addition to the DRAGOON system, the Providence Gundam is also equipped with a composite armed shield system on the left arm. This system houses a beam saber and two small beam guns. Additionally, the Providence Gundam is armed with two chest vulcan guns and can carry a "Judicium" beam rifle in its right hand.

The Providence Gundam enters combat at the end of the war on September 26, C.E. 71. It is assigned to ace pilot Rau Le Creuset, who by this point has revealed a sinister agenda. As an imperfect clone of Al Da Flaga, Rau desires to judge humanity and destroy both Coordinator and Naturals. With his powerful new mobile suit, Rau takes on his longtime nemesis (and by genetics son) Mu La Flaga. The power of the DRAGOON system proves overwhelming to Mu's outdated GAT-X105+AQM/E-X01 Aile Strike Gundam, as well as to Dearka Elsman's GAT-X103 Buster Gundam. In the final moments of the war, Rau heavily damages Kira Yamato's ZGMF-X10A Freedom Gundam and destroys his METEOR support system. However, Rau is mortally wounded by Kira's beam saber and killed by a misfire of the massive GENESIS doomsday laser. In the years after the war, ZAFT introduces a similar design, the ZGMF-X666S Legend Gundam.