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.

At a testing ground, the AEU is demonstrating its new Enact mobile suit. Suddenly, a white mobile suit descends from the sky and swiftly destroys the Enact. This intruder is the Gundam Exia, and this marks the start of Celestial Being's first mission.

As the world reacts with confusion to Celestial Being's announcement, the Gundam Meisters prepare for a second mission which will clarify their intentions.

The Union ace pilot Graham Aker confronts Setsuna as he leaves Ceylon. In Tokyo, the news reporter Kinue Crossroad begins her own investigation.

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.

Princess Marina leaves Azadistan and begins a worldwide diplomatic tour to seek help for her impoverished nation.

Celestial Being's activities have reduced the level of conflict in the world, but there are some who do not welcome this change.

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.

An international terror network has begun a campaign of bombing attacks in order to force Celestial Being to halt its armed interventions.

Four months have now passed since Celestial Being began its armed interventions. The initial chaos has subsided, and life goes on.

In Earth orbit, Sergei's mobile suit team continues its attack on the Ptolemaios and the Gundam Meisters. While Setsuna and Lockon defend their mothership, Allelujah and Tieria find themselves caught in the enemy's trap.

In the aftermath of the orbital battle, the Human Reform League's scientists realize that one of the Gundam Meisters is actually a former test subject of their own Superhuman Institute.

Although Princess Marina has secured assistance from the United Nations for her troubled homeland, the Kingdom of Azadistan is still in turmoil.

Setsuna's actions have prevented a coup d'etat in the Kingdom of Azadistan, but the conservative leader Massoud Rachmadi remains missing, and the situation continues to worsen.

The three superpower blocs begin planning a massive joint military exercise which will serve as a challenge to Celestial Being.

The Union, Human Reform League, and AEU begin their joint military exercise in the Taklamakan Desert.

On the brink of defeat, the Gundam Meisters have been rescued by the intervention of Celestial Being's second team. Their rescuers identify themselves as Johann, Michael, and Nena Trinity, the Meisters of the mysterious Gundam Thrones.

The Ptolemaios crew return to space for a rendezvous with Team Trinity. When they finally meet the new Gundam Meisters face to face, Setsuna and his comrades are disturbed by their attitude and behavior.

Team Trinity continues its campaign of armed intervention. Unlike Setsuna and his comrades, they are targeting military facilities of all kinds and exterminating everyone on the scene, even civilians.

Having determined that Team Trinity itself is promoting conflict, Setsuna confronts the Gundam Thrones. Tieria comes to his assistance, and the two Gundam Meisters fight as a team for the first time.

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.

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.

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.

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.

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 mobile armor operated by traitor Alejandro Corner.