Setsuna continues to struggle against Alejandro’s weapons and shield. Exia docks with the GN Arms and succeeds in destroying Alejandro’s shield, but the GN Arms is destroyed in the process. Meanwhile, Sergei and Soma search for Kyrios. Allelujah wishes to know the meaning of their fight and unites with Hallelujah to face the two GN-Xs. Allelujah destroys Soma’s GN-X and cripples Sergei, but does not finish them off when he recognizes Soma as someone from his past. With his mobile armor destroyed, Alejandro emerges in a golden mobile suit. Using Exia’s 7 Sword System and Trans-Am, Setsuna bypasses Alejandro’s GN Field and defeats him. Alejandro gets a message from Ribbons revealing that Alejandro was a pawn and that Ribbons is the true mastermind, right before Alvatore explodes. Graham then appears in his GN Drive-equipped Flag and engages the weakened Exia. Setsuna and Graham finally reveal themselves to each other and stab each other’s suits destroying the GN Flag but only damaging Exia. On Earth, Marina reads a message from Setsuna questioning the current state of the world and how he hoped she’d help him learn the answers. Setsuna lies unconscious as Exia floats in space.
Four years later (A.D. 2312), Saji writes a letter to Louise from space and says he is still waiting for her. He sees a GN particle trail in the distance and recognizes it as a Gundam. The UN has become the Earth Sphere Federation and all countries have disarmed and formed the ESF peacekeeping force. On Celestial Being’s asteroid base, Ian talks with Wang Liu Mei about deploying their new Gundams. Liu Mei asks to see the 0 Gundam. The 00 Gundam, which Liu Mei says will change the world, is briefly glimpsed.

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. Meanwhile, having lost over half their GN-X and the Throne Zwei, Sergei suggests the UN force withdraw. However, UN headquarters reveals that reinforcements are coming and orders a second attack. Back on Ptolemaios, the Gundams undergo repairs and upgrades. Tieria suggesting they destroy all the pseudo-GN Drives so that they can resume their original plan. The rest of the crew contemplate their pasts, but an alarm signals that the UN forces have arrived. Alejandro Corner joins the UN forces in a large, golden Mobile Armor and fires a massive particle cannon at the Ptolemaios, which barely evades the blast. With Kyrios and Nadleeh protecting the ship, Setsuna and Lasse attack Alejandro but can’t penetrate his GN Shield. Alejandro continues to fire on Ptolemaios causing massive damage. Tieria activates his Trans-Am system and destroys several GN-X, including Patrick Colasour’s GN-X, but suffers extensive damage. A GN-X manages to approach Ptolemaios and fires directly into the bridge resulting in the death of Christina and Lichtendahl. Sumeragi, Ian and Feldt manage to escape in one of Ptolemios’ containers. Lasse rams Exia’s container into Alejandro’s shield and breaks through. Exia and the GN Arms escape the destroyed container and charge back at Alejandro.

Nena Trinity mourns the death of her brothers. Alejandro Corner becomes agitated by Aeolia Schenberg’s foresight to install the Trans-Am system. 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 at the process. While returning to Ptolemaios, Setsuna detects a UN assault force approaching the other Meisters. Allelujah and Tieria deploy in their Gundams and commence battle with the GN-X and Ali Al Sarches in Throne Zwei. The Gundams activated their Trans-Am systems and destroys several GN-X, but become overwhelmed when their systems power down. Dynames arrives with its GN Arms system and destroys more GN-X suits and two UN carrier ships, but Throne Zwei destroys the GN Arms. After a vicious battle, Dynames is severely crippled. Making Haro take Dynames back to the ship, Lockon abandons his suit to chase Ali, determined to avenge his family. Using an intact cannon from the GN Arms, Lockon destroys Throne Zwei but a shot from Zwei damaged the cannon. Floating in space, Lockon contemplates that he hates the current state of the world. Before Exia could reach him, the damaged cannon explodes, killing Lockon in the process. As the remains of Dynames approach Ptolemaios, with Haro repeatedly calling Lockon’s name, the painful truth starts to dawn on the crew.

As Lockon recovers from his injuries, the UN Army announces its plan to destroy the Gundams, “Operation Fallen Angel”. The HRL’s Choubu Squadron continues to harass the exhausted Trinity siblings. Observing on Ptolemaios, the Meisters wonder if they must be destroyed to finally end war. Setsuna rejects this notion, stating that the actions of both the Thrones and the U.N. have only escalated the conflict, not solved it, and that the Gundams should stand for the eradication of armed conflict. Setsuna, wanting to learn the true purpose of the Gundams and following Lockon’s suggestion that the HRL’s attacks on Team Trinity require armed intervetion on Celetial Being’s part, goes down to Earth with Lasse in the GN Arms. Meanwhile, Ali deceives Team Trinity and hijacks Throne Zwei after killing Michael, then destroys 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 Throne Zwei. On the Moon, Alejandro gains control of Veda and discovers Aeolia in cryostasis. Taking out a golden gun, Alejandro fires repeatedly into the 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. Using the capabilities unlocked by the new system, Setsuna soundly cripples Throne Zwei, forcing Ali to retreat in hysteria.

Saji mourns the loss of his sister. Trinity launch a brief counterattack destroying one GN-X after their compound’s location is revealed. The UN Army continues its assault on Celestial Being, attacking the Ptolemaios in space. Alejandro Corner learns that the GN-Xs were created by Laguna Harvey, who is later assassinated. The Meisters’ units are out-gunned, and they struggle to defend themselves. During the battle, Alejandro accesses Veda and deactivates the Meisters’ GN Drives, leaving them defenseless. However, Sumeragi activates a backup system and every unit except Virtue is able to reactivate. Seeing Tieria’s crippled state, Patrick Colasour goes for the killing blow. Lockon manages to intercept 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 possible reproduction of the GN Drive.

The three superpowers unite to eliminate Celestial Being and form a combined military force under the UN’s command. Each of the powers receives 10 of the 30 GN-Xs, the GN-Drive powered mobile suits they found in Antarctica. However, Graham refuses to pilot one, hoping to fulfill Howard’s wish of defeating the Gundams using a Flag. Meanwhile, Kinue Crossroad encounters Ali Al Sarshes, who has just met with Ragna Harvey. Revealing her knowledge of Laguna’s involvement with the Gundams, Kinue is stabbed by Ali and left to die. Wang Liu Mei throws her support behind the Trinity Siblings. Sumeragi tells Ian to retrieve the G.N. Arms. The Thrones attack an HRL military installation, but are forced to retreat when they are overwhelmed by the HRL’s new GN-X squadron. Alejandro Corner reveals his plan to overthrow Celestial Being, with Veda being his main obstacle. Landing in a secret facility on the moon, He and Ribbons access the room containing Veda’s main core.

As Setsuna attacks the three Gundam Thrones, he is surprisingly assisted by Tieria and Lockon. Tieria reveals Gundam Nadleeh’s Trial System can disable any Mobile Suit linked with Veda. However, the Thrones manage to escape after someone hacked Veda to disable the Trial System and informing Lockon that Setsuna was once a child soldier of the terrorist organization KPSA that was responsible for the death of Lockon’s family. Lockon confronts Setsuna, but Setsuna’s explanation of his past, as well as his conviction to end warfare as a Gundam Meister, defuses the situation. Meanwhile, Louise asks Saji to return to Japan to fulfill his dream as an aerospace engineer and to move on remembering the memories as dreams, and Kinue discovers that “Ragna” refers to the president of the corporation constructing linear elevators for the Orbital Elevators. Meanwhile, as Alejandro and Ribbons continue their mysterious agenda, the three superpowers, about to surrender before the Gundams, are contacted by a member of Celestial Being to reveal a facility in Antarctica housing 30 GN Drives.

The Gundam Thrones conducted over 7 armed interventions completely destroying military bases around the world, their aggressive tactics forcing the Celestial Being observers and the Gundam Meisters aside and out of the forefront of battle. The crew of the Ptolemaios investigate the Thrones and their origins, including the possibility that Veda was hacked by an outsider to acquire the technology behind the GN Drive. On the civilian forefront, Kinue Crossroad obtains a new lead after learning that one of the Throne pilots mentioned something called ‘Laguna’. An unprovoked civilian attack by the Thrones upon a wedding in Spain forces Saji to race to Spain after Louise was severely injured (losing her left hand) from the accident, and discovers that her entire family had been killed by the attack. Later, another armed intervention upon a Union weapons factory, owned by Iris Corporation, by Gundam Throne Eins results in the deaths of 800 civilians, infuriating Setsuna as he races off in his Gundam Exia to confront the Thrones on grounds that they are supporting armed conflicts.

The Gundam Throne pilots (Johann, Michael, and Nena Trinity) meet with the crew of the Ptolemaios, and declare themselves as allies working independently of the current Meisters. However, they reveal little information about themselves and their Gundams, leaving the first meeting with strained results. Fortunately, Sumeragi reveals that she had Ian Vasty secretly inspect the Gundam Thrones. At the Union MSWAD base, Professor Eifman discovers that the Gundams’ GN particle technology may have originated from an abandoned facility orbiting Jupiter, but before he can speak of Celestial Being’s true intentions the Gundam Thrones finds out about this and kills him, the base almost completely destroyed in the process. Captain Graham and the remaining members of the OverFlags soon arrive and engage Throne Zwei, but the battle is concluded when Howard Mason is killed. The Throne’s armed intervention greatly concerns the crew of the Ptolemaios for not knowing their objectives, leaving Setsuna to question whether the Trinity siblings are really Gundam Meisters.

Three new mobile suits, piloted by a trio of siblings, appear on the battlefield and reveal themselves as Gundam Throne Eins, Zwei, and Drei. Caught off-guard by the new Gundams’ sudden arrival, the Union, AEU, and HRL forces are decimated and forced to retreat. In order to secure a route of escape, Gundam Throne Drei covers the entire region in GN particles, causing havoc with enemy communications and preventing a counterattack. After escaping from the Taklamakan Desert, the rescued Gundam Meisters are anxious about the new units and disturbed about not knowing of their existence. While world leaders despair at the appearance of the new Gundams, Alejandro Corner attends an anonymous conference with the other Celestial Being “observers” to review Celestial Being’s activities and to discuss the acknowledgement of the Gundam Thrones. Aboard their spaceship, the Trinity siblings fly to meet the Ptolemaios to greet the Gundam Meisters.