Setsuna continues to struggle against Alejandro’s weapons and shield with Lasse in the GN Arms. Exia docks with the GN Arms and succeeds in destroying the mobile armor, but the GN Arms is also destroyed in the process. Allelujah, wishing to know the meaning of their fight, unites with Hallelujah to face Sergei and Soma’s GN-Xs, but at the end of the battle is shocked to recognize Soma as someone named Marie. With his mobile armor destroyed, Alejandro emerges in a golden mobile suit to continue the fight. Using Exia’s seven swords and the Trans-Am system, Setsuna bypasses Alejandro’s GN Field and defeats him. Alejandro gets a message from Ribbons revealing that Alejandro was a pawn the entire time and that Ribbons is the true mastermind, leaving Alejandro to curse Ribbons right before his suit explodes. Graham then appears in his GN Drive-equipped Flag and battles the weakened Exia. Setsuna and Graham finally reveal themselves to each other and trade their views on the Gundams, the world, and each other. At the end of their fight, Graham and Setsuna stab each other’s suits which destroys the GN Flag, and badly damages Exia. On Earth, Marina reads a letter from Setsuna questioning the current state of the world and how he hoped she would help him find the answers. Four years later, in 2312 AD, Saji is an engineer working in the colony construction business when he takes a glance into space. And off in the distance, he sees the faint light of a Gundam…

Setsuna contemplates his memories of Lockon, who vouched for him when he first became a Meister. Tieria blames Setsuna for Lockon’s death, but Sumeragi reminds him that their true enemies are still nearby and the crew hurries to repair the Gundams. Meanwhile, having lost over half their GN-Xs and the Throne Zwei, Sergei suggests that the UN force withdraw; however, UN headquarters reveals that reinforcements are coming and orders a second attack. When Alejandro Corner joins the UN forces in a large, golden Mobile Armor and fires a massive particle cannon at the Ptolemaios, Setsuna and Lasse attack Alejandro, but are unable to penetrate his GN Shield. While the Kyrios and Nadleeh protect the ship, Alejandro continues to fire on the Ptolemaios and the Gundams, causing massive damage. One by one, the members of Celestial Being fall in battle. Tieria activates his Trans-Am system and destroys several GN-Xs, but Nadleeh is reduced to its cockpit and GN Drive while in the meantime, Allelujah continues to battle Sergei and Soma in a badly damaged Kyrios. A GN-X manages to approach the Ptolemaios and fires directly into the bridge, killing Christina and Lichtendahl. Sumeragi, Ian and Feldt manage to escape in one of the Ptolemaios’ containers as the Ptolemaios is destroyed.

Alejandro Corner, after setting off Aeolia Schenberg’s trap, becomes enraged by how Aeolia outsmarted him even in death. The Ptolemaios’ crew finish repairs to Dynames and pick up another GN Arms. The crew discuss the Trans-Am system, noting that the extreme boost in performance only lasts for a short time and drains GN particles in the process. While returning to the Ptolemaios, Setsuna detects a UN assault force, made of GN-Xs and the Throne Zwei, approaching the other Meisters. The Gundams are eventually overwhelmed by the GN-Xs, but the situation changes when the Meisters activate their Trans-Am Systems. Dynames soon arrives with the GN Arms and destroys more GN-X suits and two UN carrier ships, but the Throne Zwei destroys the GN Arms before the final blow can be dealt. When the Dynames is heavily damaged after a vicious duel with Ali, Lockon abandons his suit to continue the fight, determined to avenge his family. Using an intact cannon from the GN Arms, Lockon destroys the Throne, but a final shot from Ali damages the cannon. Floating in space, Lockon contemplates the current state of the world and admits his hatred of it. Before Exia can reach him, the damaged cannon explodes, killing Lockon in the process.

As Lockon recovers from his injuries, the UN Army announces its plan to destroy the Gundams in “Operation Fallen Angel”. The HRL’s Choubu Squadron continues to harass the exhausted Trinity siblings. Observing the situation on the Ptolemaios, the Meisters wonder if they must be destroyed to finally end war. Setsuna, wanting to learn the true purpose of the Gundams and following Lockon’s suggestion that the HRL’s attacks on Team Trinity requires armed intervention on Celestial Being’s part, goes down to Earth with Lasse in the GN Arms. Meanwhile, Ali Al-Saachez deceives Team Trinity and hijacks the Throne Zwei after killing Michael, then destroys the Throne Eins, killing Johann along with it. Ali prepares to finish off Nena, but Setsuna arrives and engages in melee combat with Ali in the stolen Throne. On the Moon, Alejandro gains control of Veda and discovers Aeolia Schenberg in cryostasis. Taking out a golden gun, Alejandro fires repeatedly into Aeolia’s capsule, but his actions set off a system trap. The trap unlocks the ‘Trans-Am System’ on the four original Gundams, giving them access to the full power and capabilities of their GN Drives. With the Trans-Am System, Setsuna is able to drive off Ali.

Saji mourns the loss of his sister, aware only that her investigations into Celestial Being were responsible for Kinue’s death. The Trinity siblings launch a brief counterattack that destroys one GN-X after their compound’s location is revealed. The UN Army continues its assault on Celestial Being by attacking the Ptolemaios in space. Alejandro Corner learns that the GN-Xs were created by Laguna Harvey, who is later assassinated by Ali Al-Saachez. The Meisters are out-gunned against the UN Army, and they struggle to defend themselves. During the battle, Alejandro accesses Veda and deactivates the Meisters’ GN Drives, leaving them defenseless. However, Sumeragi anticipates this and activates a backup system; every unit except Virtue is able to reactivate. Seeing Tieria’s crippled state, Patrick Colasour goes for the killing blow. Lockon intercepts the attack, but is severely injured. The battle ends with the UN Army retreating after losing two of their GN-X units, thanks to the timely arrival of the GN Arms. Meanwhile, the governments of the AEU, Union, and HRL consider the mission a success and begin their research into the mass production of the GN Drive.