In year 72 of the Cosmic Era, the Junius Treaty brought the hostilities between PLANT and the Earth Alliance to a formal conclusion. The treaty banned all military use of nuclear weapons and nuclear power and placed strict limits on the size of the ZAFT and Earth Alliance forces. However, there are still tensions between the genetically adjusted Coordinators and the unadjusted Naturals, and the peace between them remains fragile.

In October of C.E. 73, Cagalli Yula Athha, chief representative of the neutral Orb Union, arrives at the ZAFT military station Armory One. She is accompanied by her bodyguard, the former ZAFT soldier Athrun Zala, who now goes by the alias Alex Dino. Cagalli meets with Chairman Gilbert Dullindal of the PLANT Supreme Council to voice her concerns about ZAFT's recent arms buildup. Their conversation is interrupted as mysterious intruders attack Armory One and capture three of ZAFT's newest Gundam mobile suits.