The Ptolemaios 2 has received supplies from Katharon, and repairs are now in progress. But it cannot break through the Federation's siege without the fighting strength of the 00, and Setsuna has not yet returned to the ship. While the Ptolemaios 2 wages a defensive battle, news arrives of a coup d'etat within the Federation itself.

The Ptolemaios 2, damaged by the Innovators' attack, descends to Earth. Now separated from his comrades, Setsuna searches for the Ptolemaios 2. But instead, he finds Ali al-Saachez and his Arche Gundam waiting for him.

The Katharon space fleet has begun an assault on the satellite weapon Memento Mori, and is now under attack by A-LAWS mobile suits. The Gundam Meisters join the fray, and Setsuna engages the Innovator Hiling Care. But is this just a trick to lure Setsuna away?

The Ptolemaios 2 attempts to make a hasty escape from the attacking A-LAWS. But the Gundam Meisters are hard-pressed by Kati Mannequin's tactics and the enemy's new mobile suits. In the midst of this battle, the 00 Raiser's Twin Drive reveals its true power.

While Ian Vashti and his fellow Celestial Being mechanics prepare the O Raiser, a support machine for Setsuna's 00 Gundam, the A-LAWS deploy a devastating new weapon of their own. Tieria is outraged by the actions of Ribbons Almark and the A-LAWS, and he finally reveals the existence of the Innovators to the crew of the Ptolemaios 2.

The Federation's plan to forcibly reorganize the Middle East is opposed by the kingdom of Suille, the strongest of the Middle Eastern nations. Concerned by this resistance, the Federation decides to dispatch the A-LAWS to Suille, and Sergei Smirnov is ordered to observe the situation from the country's borders.

The year is 2312 A.D, five years after the first appearance of Celestial Being, and four years after the organization was destroyed by the United Nations forces. Thanks to the Gundam Meisters, the nations of the world have been united under the Earth Sphere Federation.

Four months have now passed since Celestial Being began its armed interventions. The initial chaos has subsided, and life goes on. Louise Halevy's mother visits Tokyo to urge her daughter to come home to Spain, Kinue Crossroad continues her investigation of the mysterious Aeolia Schenberg, and United Nations ambassador Alejandro Corner promises to aid Azadistan by connecting it to the solar power network

An international terror network has begun a campaign of bombing attacks in order to force Celestial Being to halt its armed interventions. While Wang Liu-Mei and Celestial Being's other agents investigate this network, the Ptolemaios crew watch anxiously from the sidelines, and the Gundam Meisters are placed on standby to respond to new attacks.

During Celestial Being's intervention in Moralia, Setsuna has been reunited with a figure from his past. His opponent is the mercenary soldier Ali al-Saachez, the same man who once trained Setsuna as a child soldier. Recklessly, Setsuna opens his Gundam's cockpit to confirm his enemy's identity.

Celestial Being's activities have reduced the level of conflict in the world, but there are some who do not welcome this change. Among them is the southern European nation of Moralia, whose economy is based on the arms industry and on private military companies (PMCs).

Princess Marina leaves Azadistan and begins a worldwide diplomatic tour to seek help for her impoverished nation. Meanwhile, Kinue Crossroad's younger brother Saji travels into space via the Human Reform League's orbital elevator for an educational study tour.

The Human Reform League holds a memorial service for the soldiers whose lives were lost in the recent interventions, and reaffirms its opposition to Celestial Being. Sergei Smirnov is placed in command of a new team whose mission is to eliminate the Gundams.

The Union ace pilot Graham Aker confronts Setsuna as he leaves Ceylon. Graham's Union Flag mobile suit proves to be no match for Setsuna's Gundam, but he returns from battle to learn that he and Billy Katagiri have been reassigned to a new anti-Gundam investigative taskforce.

The Celestial Being mothership Ptolemaios has been destroyed, and most of the Gundams are damaged beyond repair. Yet Setsuna continues his desperate fight against the overwhelming power of Alejandro Corner's mobile armor and the final weapon hidden within it.

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.

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.

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 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 made up of Union and AEU pilots attacks the Ptolemaios in space.

A mysterious benefactor has provided the three superpower blocs with a new weapon against the Gundams. Quickly establishing a military alliance, the superpowers organize an elite fighting force under the aegis of the United Nations.