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.

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.

The A-LAWS prepare a new trap for the reborn Celestial Being at a detention center for anti-government elements. This detention center holds the former Gundam Meister Allelujah Haptism, and the A-LAWS anticipate that Celestial Being will attempt to rescue their former comrade.

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...

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.

The Innovator Regene Regetta finally rebels against Ribbons Almark. Meanwhile, Katharon and the Federation Forces have also been drawn into the savage battle between the A-LAWS and Celestial Being. Suddenly, a giant burst of light envelops the battlefield.

The A-LAWS and Federation Forces are gathering a huge fleet to exterminate Celestial Being, and their leaders anticipate a final decisive battle. Aboard the Ptolemaios 2, Setsuna and his comrades gather their resolve for the coming battle. They each give voice to their determination, and crewmember Feldt Grace gives Setsuna a flower which once grew in his Middle Eastern homeland.

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. Ian Vashti agrees, since this will enable them to collect new equipment from Celestial Being's nearby secret factory.

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.

With the reappearance of Celestial Being, the A-LAWS begin gathering personnel who have experience fighting the Gundams. Despite their misgivings about the A-LAWS, Kati Mannequin and Soma Peries accept their new positions, promising to tell their friend Sergei Smirnov what they learn about this mysterious organization.

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 particles released by the 00 Raiser spread out across the entire battlefield.

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.

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.

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. But waiting for him there is the mysterious Mister Bushido, who has reappeared with a brand new mobile suit.

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.