In the final confrontation between Setsuna and Ribbons, the 00-Raiser is heavily damaged by Ribbons and the other Innovators; however, assistance from the other Meisters even the odds. In the ensuing chaos, Allelujah and Hallelujah work together to defeat Hilling Care, while Lockon barely manages to kill Revive Revival. Eventually, Ribbons and Setsuna damage each other to the point where neither one of them can continue fighting. However, Ribbons manages to steal one of the 00’s GN Drives, which was 0 Gundam’s, and puts it into the abandoned 0 Gundam. Setsuna, in turn, takes the remaining GN Drive and installs it back into the rebuilt Exia R2. After another difficult duel, Ribbons and Setsuna run through each other with their swords but Setsuna emerges the victor when the 0 Gundam explodes. In the epilogue, the Federation undergoes reformation as its new president disbands the A-Laws and pushes for better global peace; Saji and Louise rekindle their relationship; Allelujah and Marie leave Celestial Being to search for the meaning of their existence; Andrei Smirnov stays in the military to preserve peace like his father and mother; Patrick Colasour and Brigadier General Kati Mannequin marry; Klaus and Shirin work as politicians in the Federation Assembly; Marina returns with the children to lead a rebuilt Azadistan; Graham Aker is seen visiting Billy Katagiri in his office. As for Setsuna and Lyle, the latter now fully embracing his identity as Lockon, the two leave with Celestial Being until another armed intervention is needed as Tieria disappears into Veda to watch over the world.

The battle between the 00-Raiser and the Regnant comes to its conclusion when a Gaga attacks them both. Surviving the suicide attack, Setsuna has Saji take Louise to safety before Hilling and Revive attack the 00-Raiser. Meanwhile, inside Veda’s core, Tieria corners Ribbons and reveals that he knows the truth behind their existence before he is gunned down by Ribbons. Elsewhere, Louise finds herself in the company of Saji and attacks him, only to suffer a nervous breakdown upon finding out that he kept his ring. As the battle escalates with Hilling and Revive, Setsuna resorts to the 00-Raiser’s Trans-Am system, which triggers his abilities as a pure Innovator. As he intercepts the thoughts of his friends, comrades and enemies, he soon realizes the situation is grim. Growing frustrated, Setsuna unconsciously activates the 00-Raiser’s Trans-Am Burst system and blankets the battlefield in pure GN particles, driving Hilling and Revive off while causing a momentary ceasefire among everyone. Seizing the moment, Setsuna infiltrates the colony and closes in on Veda’s position. Meanwhile, Ribbons finds his link with Veda severed by Tieria after he joined his mind with Veda. Tieria remotely activates the Seraphim Gundam’s Trial System to shut down all units linked to Veda within its Trial Field, including the Gagas, Arche, Gadessa and Garrazo. With Veda secured, the forces of Celestial Being wrap up their battles, including Lyle as he kills Ali Al-Saachez to avenge his family and gains a new conviction. Setsuna locates Veda’s core and finds Tieria dead but no sign of Ribbons. Before he can pursue Ribbons, Tieria reveals his presence inside Veda to Setsuna and explains the entirety of Aeolia Schenberg’s plan to him. Setsuna departs for the Ptolemy but when Ribbons shoots down the Seraphim Gundam in his Reborn’s Gundam, Setsuna prepares to do battle one final time in the 00-Raiser.

Although it seemed that Regene killed him, Ribbons emerges and reveals that he used Veda to transfer his consciousness into another body. After dealing with Regene’s treachery by having Ali Al-Saachez shoot him, Ribbons reveals his massive colony ship Celestial Being and fires a massive particle cannon and destroys most of the A-Laws fleet. Celestial Being launches an assault on the Innovators’ colony ship and are countered by a swarm of Gaga units, which activate Trans-Am and launch waves of kamikaze attacks. In the ensuing battle, Patrick Colasour sacrifices himself to defend Kati’s ship and the Seravee is completely wrecked by Hilling Care and Revive Revival in their newly Trans-Am equipped suits. In the meantime, Setsuna and Saji confront Louise and Andrei; after disabling Andrei’s Ahead, Setsuna moves in on the Regnant while Saji contacts Louise. The Ptolemaios II manages to enter the colony under cover from the Arios and GN Archer, but the ship is quickly infiltrated by hordes of automatons. Lockon fights a losing battle against Ali Al-Saachez in his rebuilt Arche Gundam, while Soma’s GN Archer runs out of particles and is hit by a Gaga unit. Sumeragi heads out to face the automatons swarming the Ptolemy, but is shocked to find they were accompanied by Billy Katagiri, the supplier of the Innovators’ Trans-Am systems, who then pulls a gun on Sumeragi. Inside Veda’s core, Ribbons is stunned that Tieria managed to survive Seravee’s destruction and is now facing him at gunpoint.

The duel between Setsuna and Graham ends with Setsuna emerging victorious. However, he chooses not to finish off Graham and leaves as he tells him to live for the future. Setsuna and the others soon review Wang Liu Mei’s information and determine that a fierce battle against A-Laws will ensue as they journey to Veda’s core at L2. For this battle, Arthur Goodman has assembled a fleet of 21 ships and 108 units to crush Celestial Being once and for all. Initially, A-Laws is met with heavy resistance from Celestial Being in the form of new weapon upgrades for their Gundams. However, with particle disruptors forming an anti-GN particle cloud across the battlefield, the effectiveness of the Gundams’ beam weapons is reduced greatly. A-Laws soon breaks through their defense and only an intervention by Katharon at the last second saves the Ptolemaios from destruction. Furthermore, in a reversal of fortune, the coup d’etat forces under the command of Kati Mannequin and led by Patrick Colasour launch a counterattack and the A-Laws fleet is thrown into disarray. Soon after, Goodman is killed when his flagship is shot down by the 00-Raiser. Meanwhile, Ribbons attempts to intervene in Regene’s plans by reading his thoughts, but ends up taking a bullet to the head when Regene shoots him.

Setsuna and Saji head out to Lagrange 5 to locate Wang Liu Mei, who has, along with Hong Long, miraculously survived the attack by the Throne Drei. Nena intercepts the pair and shoots Hong Long, who sacrifices himself to allow Wang Liu Mei to escape. Liu Mei encounters Setsuna, giving him the coordinates to Veda. By the time Setsuna returns the 00-Raiser, it is taken hostage by Mr. Bushido as he reveals himself as Graham Aker and forces Setsuna to agree to a duel against him. As the battle occurs, Liu Mei is killed off by Nena as she tries to escape. But knowing she would eventually turn on them, Ribbons takes control of Nena’s Haro and tells her that someone’s coming to deliver judgement. Though expecting it to be Ali Al-Saachez, Nena is brutally killed off by Louise instead, finally avenging the deaths of her parents and relatives at the cost of her sanity. In the course of the duel, Graham and Setsuna appear to each other in an alternate reality due to the presence of GN particles. Here, Setsuna, exhibiting signs of becoming a purebred Innovator, reveals his revelation: Aeolia Schenberg created the GN Drives and Celestial Being for the sole purpose of preparing all of humanity for innovation.