Union ace pilot Graham Aker learns that he and Billy Katagiri have been reassigned to a new anti-Gundam investigative taskforce. News reporter Kinue Crossroad discovers Celestial Being's spokesman is the legendary inventor Aeolia Schenberg... a man who died more than 200 years earlier. Setsuna is sent to eliminate the remaining Human Reform League forces on the island of Ceylon. Here he encounters another formidable new opponent: veteran officer Sergei Smirnov, the dreaded Wild Bear of Russia.

The AEU and the Union seem to have reconciled themselves to the existence of Celestial Being, but the Human Reform League is still determined to eliminate it. The Human Reform League launches an operation to track down the Celestial Being mothership Ptolemaios. Sergei Smirnov and his Chobu special forces team deploy huge numbers of tiny probes in Earth orbit. Sergei and Sumeragi match wits in a series of tactical feints, and Sumeragi realizes too late that the enemy's true objective.

Kinue's younger brother Saji and fellow student Louise travel into space for a study tour. The Human Reform League begins a performance test of the Tieren Taozi, an experimental mobile suit designed exclusively for super soldier Soma. Allelujah is sent to observe the test, but he and Soma react strangely to each other's presence. When Soma loses control and opens fire on the nearby low orbital station, Saji and Louise find themselves in deadly danger.

An international terror network has begun a campaign of bombing attacks in order to force Celestial Being to halt its armed interventions. Princess Marina's diplomatic tour has now brought her to Scotland, where she encounters Setsuna in the aftermath of another terror attack. Meanwhile, the AEU and Union intelligence agencies provide Celestial Being with information on the terror network, allowing the Gundam Meisters to go into action against the terrorists.

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. The AEU decides to hold a joint military exercise with Moralia as a show of support. Celestial Being prepares to intervene in this joint exercise. As the Gundam Meisters go into battle against a combined AEU, Moralia, and PMC force of more than a hundred mobile suits, Setsuna encounters a familiar adversary.

The Human Reform League holds a memorial service for their dead. Sergei is put in command of a new team whose mission is to eliminate the Gundams. The team's trump card is a young woman, Soma Peries, Super Soldier Number 1. An international crisis begins as the South American nation of Taribia declares its independence from the Union. In the Kingdom of Azadistan, Princess Royal Marina Ismail anxiously watches the crisis unfold. The fate of her homeland may depend on how Celestial Being responds.

As the world reacts with confusion to Celestial Being's announcement, the Gundam Meisters prepare for a second mission. While Allelujah and Tieria descend from space, Setsuna and Lockon make contact with the Celestial Being agent Wang Liu-Mei, and all four Gundam Meisters then join forces for an armed intervention on the island of Ceylon.

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. The Gundam Meisters force the Moralian forces to surrender. Celestial Being tactical forecaster Sumeragi Lee Noriega is troubled by the knowledge that this mission has cost hundreds of lives, and more are soon lost as a worldwide series of terror attacks begins in response to Celestial Being's activities.

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.

Setsuna begins a final decisive duel. Lyle's intentions, Allelujah's hopes, and Tieria's thoughts flow through the darkness of space. The particles from the 00 Raiser envelop the area around them…

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. Meanwhile, Katharon hopes to join forces with Suille, and begins negotiations with the kingdom.

Setsuna and Tieria are confronted by Ali al-Saachez and his new Arche Gundam. A furious Tieria tries to avenge Lockon, but is overwhelmed by the enemy's fighting strength. From Tieria's behavior, Lyle learns that al-Saachez is the man who killed his brother.

Tieria is shocked at the sudden appearance of his lookalike Regene Regetta. He is further disturbed by Regene's revelations about the Innovators. When the Celestial Being members receive information that top A-LAWS members will be attending an upcoming party, Tieria joins Setsuna to infiltrate the party on a reconnaissance mission.

Sumeragi has regained consciousness, and thanks to her tactical plan the Ptolemaios 2 is able to escape the battlefield. However, Allelujah's Gundam has been shot down along with Soma Peries, and his comrades cannot locate him. Allelujah and Peries leave their crashed mobile suits and confront each other in person.

The Katharon base has been devastated by the A-LAWS attack. The words of a dying soldier remind Sumeragi of a traumatic incident from her past, and she passes out. Meanwhile, Kati Mannequin is horrified by the results of Aber Rindt's ruthless mopping-up operation. Soma Peries is also despondent after witnessing the attack. She receives a message from Sergei Smirnov, but although she appreciates his sympathy, she sees no choice but to accept her role as a super soldier and recommit herself to the battlefield.

Having been rescued from near defeat by the Katharon resistance group, the Ptolemaios 2 now takes refuge at a Katharon base in the Arabian desert. Resistance leader Klaus Grad offers to join forces with Celestial Being against their common enemy, but the crew are reluctant to ally themselves with Katharon. While Setsuna takes off in a small craft to return Marina to Azadistan, Saji takes this opportunity to part ways with Celestial Being. Saji is quickly captured by regular Federation forces under the command of Sergei Smirnov, and reveals the location of the Katharon base. When this information is passed on to the A-LAWS, they launch a ruthless mopping-up operation, and the warriors of both sides are horrified by the results.