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Taking place a few months after the end of the second season, an unknown alien fragment appeared out of Jupiter and landed on a research space station in its orbit and reactivates the ship, causing it to move slowly and heading towards Earth. In Celestial Being's Asteroid Base, Ian Vashti greeted his wife, Linda, after her 2-year assignment and unloading two new GN Drives and a new incomplete Gundam, the GNT-0000 00 Qan[T].
In the 2 years that has passed since the defeat of the "Innovators" and A-Laws, Saji Crossroad arrived at an Earth Federation Hospital to be with Louise Halevy, who is still in medical care due to physical changes by the Innovators, while still thinks about what has happened with Celestial Being. At the same time, Marina Ismail and Shirin Bakhtiar inspected a colony construction facility when their shuttle was nearly attacked by an assassin, piloting a GNX-609T GN-XIII. However Setsuna F. Seiei arrives in a customized Flag and destroys them, with Lockon in the cockpit stopping the assassin from killing Marina and left with Setsuna.
Meanwhile, the Earth Sphere Federation had discovered a Jupiter research station heading towards earth and sends out GNX's Mobile Suits, led by Andrei Smirnov, to destroy it. Kati Mannequin arrived on board the Celestial Being station with Patrick Colasour and encounter Veda and its surviving Innovades, now serving the Federation to maintain the mothership, and later meets a newly emerging Innovator, Descartes Shaman. When a Federation staff reports the probe ship still heading towards earth despite being hit by multiple GN missiles, Descartes heads out and pilots the GNMA-Y0002V Gadelaza, successfully destroys the ship with the debris falling to earth. Not long afterward, Earth's population experienced a series of unusual events, with electronic vehicles and devices operating on their own. Later a girl arrived at her home, only to have her left hand partly turned metal and encountered a man in a space suit reaching towards her as she screams.
Billy Katagiri meets with Meena Carmine to analyze the young girl whose body has partially assimilated. Deducing that the events occurring are related to the alien lifeforms earlier, now dubbed the Extraterrestrial Living-metal Shape-shifters (ELS). During this time, Setsuna and Louise's quantum brainwaves kept giving them ominous feelings about developing events and Setsuna's concern magnified when Ptolemaios crew was unable to contact Allelujah and Marie, with Lockon and Setsuna heading off.
In the Earth Federation Hospital, Saji witness a blackout in the building with Louise started screaming as the appearance of a man in a spacesuit appeared. Saji knocked him down and escape with Louise while passing by an unconscious hospital staff, however the man tossed Saji and was about to reach to Louise until Setsuna appeared and shot the man's visor and was shocked to reveal the man was Ribbons Almark. As Setsuna kept on shooting him as he continues to walk towards him, he threw a plastique on him, which caused Ribbons to explode, but left only the bottom half moving until it shatters into liquid metallic fragments. With Saji holding Louise and asking Setsuna what has happened, which he replied he does not know. In Mongolia, a traveling Allelujah Haptism and Marie Parfacy were attacked and chased by living technology infected by the ELS. While running away from them, they see a group of Innovators that are being assimilated, and a van that was previously destroyed regenerate itself. Due to the quantum brainwave interference from the ELS, Allelujah switches personalities to Hallelujah to manage the mental stress and cause the ELS to go after him, however Lockon Stratos arrived in the GN-002RE Gundam Dynames Repair and destroyed them.
Not long afterwards, the very same Jupiter research station they thought had been destroyed reappeared and Celestial Being takes the offensive. Setsuna heads out in the 00 Raiser Condenser Type, along with Lockon in his new Gundam, the Zabanya, and Allelujah paired with Marie in the Gundam Harute and confront the ELS. Problems began to arise when Setsuna is unable to fight the ELS due to quantum brainwave interference. Compromised in battle, 00 Raiser's left arm and shoulder binders are hit and being slowly assimilated. However, Tieria Erde arrives in the Raphael Gundam and rips out 00 Raiser's infected left arm, allowing Setsuna and the team to escape. Unknown to both the Federation and Ptolemaios crew, the ELS had begun launching its forces from Jupiter's Big Red Spot, sucking in Io and Ganymede.
The Federation forces later traveled to Mars in order to discover the ELS's intentions, with Descartes heading out first in the Gadelaza and destroying most of them before the Federation's Mobile Suits forces had engaged in battle, however most of its ships and Mobile suits were assimilated, and Descartes who had destroyed almost all of the ELS was assimilated as well, killing him in the process. Celestial Being arrived too late to save the Federation soldiers and engaged in battle against them. Setsuna executes Trans-Am Burst in an attempt to communicate with the ELS, theorizing that this is the "dialogues to come" that Aeolia Schenberg was conditioning humanity for. Unfortunately, Setsuna falls victim to a mental attack from the ELS and is rendered comatose in the middle of battle, with the 00 Raiser being hit by the ELS from all directions. Tieria is forced to reveal Raphael Gundam's backpack, GN-008RE Seravee Gundam II, and forcibly rips 00 Raiser's cockpit from the frame, handing it to Lockon as Tieria tries to hold off the ELS with his quantum brainwaves. With the ELS surrounding him and assimilated both his physical body and the Raphael, Tieria activated it's Trans-Am and set it to overload, causing the Raphael to self-destruct and taking most of the ELS with him, however most of them survived but was destroyed by The Sol Brave Squadron, led by Graham Aker, and escape with the Ptolemaios. Tieria's conscious mind returns to Veda and Feldt Grace desperately awaits at Setsuna's side to awaken. After the battle, the Ptolemaios crew and the Earth Sphere Federation witness the appearance of a large moon-size ELS, with Feldt announcing it will head towards Earth in 92 days.
With most of the civilians being informed of the situation and heading towards shelters, Saji who watch the whole situation tells Louise that he's going on the Orbital Elevator to help fight the ELS as the last line of defense. In the day of the ELS's arrival, the Federation launch a counterattack against the ELS using the Celestial Being ship's main cannon. Kati, in charge of the operation, ordered to fire its main cannon, which has damaged the ELS superstructure. During this time, Tieria makes a request to Ian Vashti that a miniature Veda terminal be installed in the cockpit of 00 Qan[T] to handle the massive amounts of information that would result from linking with the ELS again. It was also the moment Mileina Vashti confesses her love for Tieria.
During the battle, many of the Federation's Baikal-class ships and GNX-803T GN-XIVs were assimilated by the ELS, who subsequently created their own copies of the technology. Zabanya and Harute then arrived to assist the ESF in battle. Lockon uses the Zabanya's GN Rifle Bits and GN Holster Bits to destroy the ELS en masse, while Allelujah and Hallelujah combined once again, enhancing the performance of the Harute through the Marute System. Despite the much needed backup, the ELS still overwhelms the ESF forces and assimilates many ships and Mobile Suits. Meanwhile, on board the Ptolemaios 2, a still-comatose Setsuna lies in a dream-like state. There, he has visions of the first Lockon, Christina Sierra, and Lichtendahl Tsery. Setsuna then sees the flower that Feldt gave him and finally wakes up, finding Feldt at his side. After Setsuna fully recovered, he sorties in the GNT-0000 00 Qan[T] for battle, while Feldt returns to the bridge.
In battle, Patrick's GN-XIV was hit by an ELS and is slowly assimilated as he prepares to self-destruct before saying goodbyes to Kati, when 00 Qan[T] blasts Patrick's GNX, saving him from assimilation. Andrei Smirnov noticed one of the ELS ships heading straight for Earth and used Trans-Am in its overloading state, self-destructing his GNX and destroying the ELS ship it at the cost of his life. With a large number of ELS appearing despite the Gundam destroying most of them, the Harute was eventually assimilated and Allelujah and Marie are forces to abandon Harute. Setsuna attempts to communicate with the ELS via the Twin Drive's quantum effect, but it is to no avail as the ELS constantly thwart Setsuna's attempts. Tieria, now a small hologram inside of the 00 Qan[T], tells Setsuna that Trans-Am is necessary for the dialogues. Graham Aker, now partially assimilated, decides to believe in a better future for humanity and sacrificed himself to create a large hole using Tr