Celestial Being, a private army dedicated to eradicating war, begins demonstrating the powers of their new "MS-GUNDAM" suits by interrupting the public demonstration of AEU's latest Mobile Suit, the AEU Enact and by protecting the Human Reform League's Space Elevator, "Tenchu" from being attacked by terrorists when their mobile suits had attempted to launch rockets on the "Tenchu", earning a news appearance from various TV news channels where Celestial Being's goals were publicly stated by Aeoria Schenberg.

The world bodies discusses the possible origins and impact of Celestial Being. The Gundams made their first combat appearance in Ceylon, formerly called Sri Lanka where Lockon leads the Gundams in taking on the Human Reform League and rebel Sri Lankan forces. Meanwhile, JNN reporter Kinue Crossroad discovers something about Aeoria Schenberg's origins. The episode ends with Graham Aker ambushing Setsuna to sate his curiosity about the Gundams.

Setsuna dispatches Graham with ease, the latter being caught off guard by the advanced technology of the Gundams. Tieria returns to space with Gundam Virtue. The Union Army creates the Anti-Gundam Investigative Squad with Graham and Billy transferred from the MSWAD as official members. Meanwhile, Celestial Being launches surprise attacks in South Africa, the South American continent over Taribian airspace, formerly in Venezuela and Guyana, and in Ceylon. Setsuna later faces off against Colonel Smirnov while conducting an attack against Human Reform League mobile suits. Later on, a JNN broadcast revealed that various militant factions in North Ireland signed a peace treaty, ending years of fighting between themselves, the British Army and the PSNI.

Colonel Sergei returns to the Reform League to head a new squad designated for capturing one of the Gundams, with Soma Peries as his designated subordinate. Encouraged by Celestial Being's anti-conflict actions, the South American nation of Taribia declares its withdrawal from the Union and declares it independence over the control of energy resources, prompting a Union military response, forcing Celestial Being to intervene. In Azadistan (In the territory of Iran), Shirin Bakhtiar explains to First Princess Marina Ismail that the conflict is not as simple as it may first seem. Meanwhile, the Anti-Gundam Investigative Squad, in Flag Customs, engage Exia in Taribian airspace. Later on, pro-Taribian separatist politicians led by its prime minister are forced to drop their bid for independence after their forces were defeated by the Gundam Meisters.

Colonel Sergei conducts tests on a new Mobile Suit built especially for Soma Peries, a bioengineered human. Allelujah Haptism and Soma Peries experience a strange connection brought on by their proximity to each other. This causes Soma Peries to go into a fit of rage who begins to fire shots randomly at the space elevator severing a section containing civilians. Meanwhile on board the elevator Allelujah Haptism experiences another side of himself but regains his composure and runs off. Colonel Sergei attempts to help the civilians before they drift past the Breakaway Limit Zone and into the Earth's atmosphere but his mobile suit is ill-equipped. Allelujah Haptism, piloting the Gundam Kyrios, arrives to aid the Colonel.They save the civilians but at the cost of revealing Dynames' GN Sniper Rifle Extreme Long Range Custom.

The Republic of Moralia, located in the southeast of France (what today is the Principality of Monaco) and a member of the AEU, has placed in armed forces in joint exercise with French-led AEU forces, including Patrick Colasour. Marina heads to France to request humanitarian assistance, despite the incomplete status of the AEU's Orbital Elevator. Meanwhile, Celestial Being Gundam Meisters were led by Sumeragi Noriega and her crew (except Lichtendahl Caeli and Lasse Aion) alongside Wang Liu Mei in disrupting the exercises, taking on both Moralian and AEU mobile suits. Later on, Setsuna is surprised when he takes on Ali Al-Saachez, a figure from his past, in his custom-made AEU Enact prototype.

The Gundam Meisters were able to defeat the Moralian Army, despite an earlier attempt by Setsuna to confirm if Ali was in the AEU Enact prototype that he fought with. Their actions had formed the Moralian Armed Forces to surrender to the Meisters after the previous State of emergency was declared. While Setsuna was being reprimanded by Lockon and Tieria for placing all of Celestial Being in danger for the potential of having their real identities exposed, an unknown terrorist group had conducted simultaneous bombings in various nations as a warning message to take on Celestial Being with more indiscriminate bombings unless the group disbands.

The Gundam Meisters are being sent off to investigate the terrorists responsible for the indiscriminate bombings in the Union, HRL and AEU. In Scotland, Setsuna attempts to capture one of the bombers, but was nearly apprehended by a Scottish Authorised Firearms Officer after firing his pistol if not for Marina's intervention.

It has been four months since Celestial Being's first intervention and the Gundam Meisters have been involved in over sixty intervention operations. As the world begins to change around them, the crew aboard the Ptolemy and the Gundam Meisters have some time to themselves.

The HRL's operation against the Celestial Being continues. Allelujah again becomes disorientated by his proximity to Soma Peries resulting in the capture of Kyrios. Tieria arrives to find the captured Kyrios within a transport vessel. As he attempts to destroy the vessel before it escapes the Virtue is overwhelmed. Meanwhile, Allelujah's other half Hallelujah awakens and destroys the transport ship he is inside. He then goes off to face Soma Peries and Sergei Smirnov, but they escape. The battle finally ends though it is a Pyrrhic victory for both sides, with Tieria revealing one of the Celestial Beings greatest secret GN-004 Nadleeh and the HRL losing many mobile suits in return. With the near capture of Kyrios and Ptolemaios' close escape, Celestial Being is shaken to the core with the majority of its members saddened by the experience.

Allelujah Haptism decides to face his past and proposes a mission to destroy the facility where he was 'created'. Sumeragi accepts his proposal and launches Exia and Dynames to attack South Africa as a diversion while Kyrios and Virtue assault the HRL colony where the illegal experiments on children have been conducted. Flashbacks of Allelujah's turbulent past is shown as he grapples with the decision to open fire on the experimental lab. Celestial Being then leaks information on the experiments to the media, turning it into an international incident and a public relations disaster for the HRL. Sergei becomes aware of the experiments and detains one of the scientists responsible and who also tried to cover it up. Kinue also continues her investigation into Aeolia Schenberg, delving deeper into the mysteries surrounding Celestial Being's founder.

An Imam named Massad Rachmadi was kidnapped by an unknown armed group, which led to riots by the Azadistani populations against the military called in to guard the city. Celestial Being and the Union Army began to intervene when radical factions in the Azadistani military began to attack loyalist forces guarding the Solar Antenna to link up with the Orbital Elevator. As Celestial Being and Graham's forces, grudgingly, face off against rebel Azadistani mobile suits, Setsuna is forced to re-live the events of his traumatic past after encountering Azadistani military mobile suits attacking armed children.

With the whereabouts of Massad Rachmadi unknown, Azadistan falls into a state of civil unrest with constant terror attacks. Reviewing the previous battle, Lockon reveals the possibility that there may be a third force aside from the Union-Azadistan forces and Celestial Being. After Setsuna and the duo of Graham and Billy investigate the possible site of where missiles had been launched by Ali, Setsuna deduces that location of where terrorist forces, led by Ali himself, are located. Setsuna and Lockon, with the assistance of Hong Long, attack the terrorist hideout. Setsuna manages to hold his own against Ali, who manages to escape from the battle, while Lockon and Hong Long utilizes the distraction to rescue Rachmadi. Deciding to display a show of bravado, Celestial Being authorizes Setsuna to deliver Rachmadi to the Azadistan royal palace with Exia unarmed. Despite pressure from present Union and Azadistan forces, the hostage release is successful. Marina asks the pilot of Exia if he is truly Setsuna, to which Setsuna vaguely encourages Marina to take up the fight for peace in Azadistan.

With Ptolemaios undergoing maintenance the members of the Celestial Being take a short day off on Earth. Meanwhile the Union, AEU, and the HRL hold a secret meeting to discuss plans for "Project G", a joint project of the three groups to try to capture or destroy the Gundams. From the public's point of view it is stated as a joint military exercise by the three groups. Information later comes in that the three armies will converge at a point in the Taklamakan Desert with a high risk of spreading nuclear radiation around the world if careful measures aren't taken. Celestial Being decide to intervene, fully knowing the true objective of the enemy's plans and that they are extremely outnumbered and that they may not come out unscathed. Meanwhile, Setsuna takes a short detour to Azadistan to ask and listen to Marina's opinion of why the world is so distorted.

As planned, Celestial Being begins their armed intervention in the Taklamakan Desert against a combined force of nearly a thousand mobile suits from the Union, AEU, and HRL. Immediately upon involving themselves, the four Gundam Meisters are attacked and face a ruthless bombardment from the allied forces for nearly fifteen straight hours. Exhausted and pushed to the limits of their abilities, the Meisters then find themselves pitted against ace pilots sent from the allied forces, with the intent of capturing them. Outnumbered and overwhelmed, the Gundams are one by one disabled and deactivated, until only Setsuna remains. Then, just as he's about to be finished off, a mysterious mobile suit, emitting red wing-like GN particles, appears and drives the enemy away.

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.

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 two groups first meeting with strained results. However, Sumeragi later reveals that she had Ian Vasty secretly obtain information about the Gundam Thrones.

The Gundam Thrones continue to attack military installations around the globe, 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 'Ragna'.

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 informing Lockon that Setsuna was once a child soldier of the terrorist organization 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 Livonze 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 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.

Saji mourns the loss of his sister. The Trinity siblings are betrayed and launch a brief counterattack after their compound's location is revealed, destroying one of the 10 GN-X units from Choubu's assault force. The UN Army continues its assault on Celestial Being, attacking the Ptolemaios in space. Raguna Harvey is killed after Corner learns that it was he that created and sold the GN-X units. The Meisters' units are out-numbered, and they struggle to defend themselves against the GN-Xs firepower. During the battle, Alejandro Corner accesses Veda and deactivates the GN drive of the Meisters' units, leaving them defenseless. However, Sumaragi activates a backup system and every unit except Virtue is able to reactivate. Seeing Tieria's crippled state, Patrick Colasaur goes for the killing blow. Lockon is able to intercept the attack, but is severely injured. The battle ends with the UN Army retreating after losing two of their GN-X units, and the timely arrival of the GN Arms.

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.

Nena Trinity mourns the death of her brothers. Meanwhile on the moon Alejandro Coroner becomes incresingly agitated by Aeolia Schenberg's foresight. The crew of the Ptolemaios finish repairs to Dynames and pick up another GN Arms from its asteroid base within the Laragne 1 resource asteroid belt. The crew discuss the Trans-Am system, commenting how it provides a boost to performance, but only lasts a short time before the GN Drive must replenish the spent energy. Setsuna and Lasse make their way back to Ptolemaios and detect UN carrier ships heading to the Meisters' location. Warned of the attack, Allelujah and Tieria deploy in their Gundams, but Lockon is prevented from leaving. The battle soon commences between the Gundams and GN-X along with Ali Al Sarchez in the Gundam Throne Zwei. Allelujah and Tieria activate their Trans-Am systems and quickly destroy numerous GN-X. However, they become overwhelmed when their Trans-Am systems power down. Relief appears in the form of Dynames docked with its GN Arms system. Lockon uses the weapons platform to destroy more GN-X and two of the carrier ships before it is destroyed by Ali. Lockon chases after Ali determined to avenge his dead family. Zwei and Dynames engage in a vicious battle and Ali manages to cripple Lockon's Gundam. While Lockon makes Haro pilot the suit back to Ptolemaios, he exits the Gundam with his targeting rifle. Using an intact GN Cannon from his destroyed GN Arms, Lockon succeeds in destroying Zwei, but a shot from Zwei also damages the Cannon. As Lockon floats nearby he thinks about the world, its state and how he dilikes the current world. Holding his hand out to the world he questions those living on the Earth, if they like the current world because he doesn't. The GN Cannon explodes killing Lockon. Celestial Being suffer their first devestating loss leaving Setsuna to scream into the depths of space.

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.

Setsuna continues to struggle against Alejandro's weapons and shield. Exia docks with the GN Arms and evens the odds with the Alvatore. Setsuna 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 damaged, Alejandro emerges in a golden mobile suit. Setsuna uses Exia's 'trump card' (his physical GN Blade) to bypass Alejandro's GN Shield and defeat him. Alejandro gets a message from Livonze revealing that Alejandro was a pawn and that Livonze is the true mastermind, right before Alvatore explodes. Graham then appears in his GN Drive-equipped Flag and engages Setsuna. Setsuna and Graham finally reveal themselves to each other and destroy each other's mobile suits. On Earth, Marina reads a letter 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 mobile suits. Liu Mei asks to see the O Gundam, the first generation unit, and then comments that the OO Gundam will change the world.