C.E. 73. 2 years have gone by since the war ended. Gilbert Dullindal leads ZAFT after the death of Patrick Zala. An Orb-born Coordinator, Shinn Asuka, becomes the newest topgun of ZAFT after Athrun's departure. His eyes reflects sorrow perhaps because he is lonely and lost his family. He himself represents the "War's Tragedy". Why did he join ZAFT and try to enter the battefield? Revenge? A mission? No one knows. Meanwhile, Athrun is part of Orb and right beside Cagalli. He worries both about the heavy burden of protecting Cagalli and the feeling to do something about the world.

One who joined ZAFT and one who left. The story begins when the two cross.

The Junius Treaty was signed in the first half of C.E. 72 at the place where Junius Seven once stood onboard an Earth Alliance battleship. There, ZAFT built a monument to the treaty. The details of the treaty itself state that both sides were to ban the use of Neutron Jammer Cancellers and the Mirage Colloid. Both sides also agreed to set a quota restraint on the size of their MS forces. Despite that, the two continued to research and develop new weapons due to the lingering bitterness between them. Because of the MS force limit, an emphasis on quality rather than quantity came about, leading to more advanced MS.