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.

With the reappearance of Celestial Being, the A-LAWS begin gathering personnel who have experience fighting the Gundams.

The A-LAWS prepare a new trap for the reborn Celestial Being at a detention center for anti-government elements.

Setsuna and his comrades have successfully overpowered the A-LAWS and freed Allelujah and Marina from the Federation's detention center. When Marina asks them to return her to Azadistan, they set a course back to the Middle East.

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.

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.

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.

Tieria is shocked at the sudden appearance of his lookalike Regene Regetta. He is further disturbed by Regene's revelations about the Innovators.

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.

The Federation's plan to forcibly reorganize the Middle East is opposed by the kingdom of Suille, the strongest of the Middle Eastern nations.

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.

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.

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 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 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.

The A-LAWS have abruptly retreated after receiving word of a coup d'etat within the Federation. Hoping to reunite with his comrades, Setsuna sets the 00 on a course for Africa.

A crisis is unfolding, but the Ptolemaios 2, which has not yet been fully repaired, is unable to break the deadlock. The wounded Setsuna returns to battle despite his injuries, asking Saji to help him save countless innocent lives.

Four months have passed since the "Break Pillar" incident, the near-collapse of an orbital elevator. The A-LAWS leaders receive word that Celestial Being has resumed activity after months of silence.

As Saji Crossroad searches for Louise Halevy amid the chaos of battle, Soma Peries hunts for Andrei Smirnov in order to avenge Sergei's death. Setsuna confronts the Innovator Hiling Care and unleashes the power of the Twin Drive.

The Innovator Revive Revival is now a prisoner aboard the Ptolemaios 2, but he sneers at the questions of its crew, and gives them nothing but evasive replies. Suddenly, the crew receive word that crewmember Mileina Vashti has been taken hostage.

The Ptolemaios 2 has received a message containing coordinates for a point at Lagrange 5. The crew are suspicious, but Setsuna suggests they set course for this mysterious location.

The Innovator Regene Regetta finally rebels against Ribbons Almark.

As Tieria enters the enemy ship and learns shocking truths, the Ptolemaios 2 fights a defensive battle against the unrelenting enemy assault. One by one, our heroes fall. Setsuna cries out as if responding to the fading light of their lives.

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.