In year 72 of the Cosmic Era, the Junius Treaty brings hostilities between ZAFT and the Earth Alliance to a formal conclusion, but the peace remains fragile.

With Armory One under attack, Athrun commandeers a ZAFT mobile suit. He's engaged by the three captured Gundams, but is rescued by the sudden appearance of young ZAFT pilot Shinn Asuka and his Impulse Gundam.

Shinn and Rey struggle against the enemy commander Neo Roanoke. ZAFT Captain Talia Gladys orders the newly constructed warship Minerva to launch from Armory One and join the battle.

The Minerva follows the Girty Lue into the debris belt surrounding Earth, sending Shinn and his comrade Lunamaria Hawke in pursuit of the enemy mothership.

Aboard the Minerva, Chairman Durandal receives shocking news that the ruins of planet Junius 7 have left their stable orbit and begun falling toward Earth.

The Minerva launches mobile suits to support Yzak and his demolition crew. Shinn, Rey, Lunamaria, and Athrun join the battle against the mysterious group who've sent Junius 7 plunging toward Earth.