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. But the A-LAWS have anticipated this course of action as well, and they are already deploying a powerful new mobile armor to ambush the Ptolemaios 2 in the Arabian Sea. As the two sides prepare for battle, their members are becoming aware of their connections to the enemy. Allelujah is convinced that Soma Peries, whom he met at the detention center, is his childhood friend Marie. Kati Mannequin, meanwhile, has begun to suspect the true identity of Celestial Being's tactical forecaster. And Billy Katagiri, whose love for his old friend Sumeragi has now turned to bitter hatred, makes a fateful decision.

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. Among the other prisoners is Marina Ismail, princess of Azadistan, who has her own connection to Celestial Being. In space, the Ptolemaios 2 crew learn of Allelujah's whereabouts, and ask the reluctant Sumeragi to draft a rescue mission plan. As the ship plunges down into the atmosphere to carry out a daring five-minute raid on the detention center, the Gundam Meisters of the reborn Celestial Being prepare for their first battle as a genuine team.

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. Meanwhile, Setsuna is recruiting members for the reborn Celestial Being. Traveling to Earth, he makes contact with Lyle Dylandy, twin brother of the late Lockon Stratos, as well as the former tactical forecaster Sumeragi Lee Noriega. But as Setsuna and his comrades return to the Celestial Being mothership Ptolemaios 2, they find that it is already under attack by the A-LAWS. Only the power of an untested new Gundam can save the day...

The anti-Federation resistance group Katharon launches a daring raid on the space colony Proud, in order to free their comrades who are being held there. Among the prisoners at Proud is a young space engineer named Saji Crossroad who has been arrested by the government's overzealous security forces. However, the A-LAWS have anticipated Katharon's rescue mission, and they deploy unmanned killing machines to wipe out the prisoners. In the middle of this chaos, Saji is reunited with his former neighbor Setsuna F Seiei.

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.

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, 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. While the Ptolemaios 2 wages a defensive battle, news arrives of a coup d'etat within the Federation itself.

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.

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.

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.

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.

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. Ian Vashti agrees, since this will enable them to collect new equipment from Celestial Being's nearby secret factory. Meanwhile, Hiling Care and the other Innovators are vexed by the power of the 00 Raiser, which they now suspect is due to more than just the capabilities of the mobile suit itself.

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 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.