The Celestial Being mothership Ptolemaios has been destroyed, and most of the Gundams are damaged beyond repair. Setsuna continues his desperate fight against the overwhelming power of Alejandro Corner’s mobile armor and the final weapon hidden within it. One last enemy, however, is waiting for him in the darkness of space. A new world is about to be born from this destruction. Years later, the true form of this world reformation will become apparent, and a new Gundam will appear on the stage.

Despite the loss of Lockon, the Ptolemaios crew are united in their determination to keep fighting the United Nations forces. The enemy begins another assault, this time spearheaded by the Alvatore, a giant mobile armor operated by the traitor Alejandro Corner. As Allelujah and Tieria engage the remaining GN-X teams, Setsuna loads the Gundam Exia into an assault container and sets off to eliminate Alejandro’s mobile armor.

Alejandro Corner and Ribbons Almark have forced their way into the heart of Veda and taken control of Celestial Being’s master computer. But their actions have triggered an unexpected programmed response. In a recorded message, Aeolia Schenberg has named the Gundam Meisters as his inheritors and entrusted them with the full power of the GN Drive. Now that the Trans-Am system has been enabled, the Gundams may yet be able to fight off the greater strength of the UN forces.

The United Nations reveals the existence of the GN-X to the world, and announces the launch of a Gundam elimination operation with the code name “Fallen Angels.” The operation begins with the renewed pursuit of Team Trinity, who have been forced to abandon their supply base and can now only flee before the enemy’s superior numbers. The mercenary soldier Ali al-Saachez approaches the Trinity siblings, presenting himself as an ally, but his true mission is one of assassination.

The United Nations forces have deployed their new weapon, a mobile suit model known as the GN-X which is powered by a pseudo solar reactor. While Sergei Smirnov and Soma Peries lead a GN-X team in pursuit of the Gundam Thrones, another force attacks the Ptolemaios in space. Orchestrating all this is Alejandro Corner, the rogue Observer who has betrayed Celestial Being. Having provided the United Nations with its powerful new weapons, Alejandro now enters the very core of the supercomputer Veda.