Van and Wendy are surprised to see The El Dorado Five at the rendezvous point, along with Carmen 99, Yukiko, Joshua, and Priscilla. After they all agree that they must stop The Claw, Carmen 99 sets up coordinates on the data disk in the hover-base, while getting money for supplies through a man named Manson. They are guided to a seaport kingdom near Missoghi controlled by its queen Catherine Nakata, where the initial plan is to capture her and sail through. However, they are invited to participate in a swimming challenge, to which they accept. Wendy faces off against Marianne to a race, and, with the help of Kameo, is able to reach the goal. Meanwhile, Manson explains to Joshua that he and the queen were once business partners in marriage, working together to develop an innovative metallic fiber. However, Manson had rejected her idea of creating underwear using the fiber, which had led her to build a bikini kingdom prospered by women. Fasalina is seen making a transaction with Catherine for materials called the "impregnable armor stock". After the race, Carmen 99 and Fasalina cause the kingdom to crumble from underground, as everyone evacuates. In the end, Manson reunites with Catherine after sporting her metallic underwear prototype.
Michael finds himself caught inside a bluish fluid shell on the moon that serves as a destroyer system, finding a deceased crew surrounding a spaceship, formerly the comrades of The Claw who had been trying to achieve colonization on the moon, but they had ended up murdering each other. Michael begins to transmit the destroyer system from the moon to the world. Van, inside Gadved's satellite base, is starts the restoration process of his armor. The protagonists at the hover-base make their way towards The Claw's base-of-operations, set to take seven days to arrive there. Not only has the moon changed color, but it also seems as if it is falling out of orbit. Fasalina comes to stop them and commands her army of knight armors to attack. A blind Ray uses his Vulcan guided by Joshua to wipe them out. Van, now recuperated, briefly battles against Michael in outer space, confronting their differences.
Upon arriving at Zonnet Junction, Wendy is shocked to find her brother Michael at the train station. Van and Joshua lose track of Wendy when the train passes by, having to split up to go search for her. Wendy is surprised to know that Michael has sided with The Claw, thereby supporting his cause. Michael then tells Wendy to return back home to Evergreen as he departs. After Carmen 99 meets up with Joshua, the two see an angry Van after hearing that Wendy saw her brother but did not inform him, hence missing a crucial opportunity to find The Claw. He tells Wendy to go home like her brother suggested since she has no reason to go on anymore. Meanwhile, the metal coffin retrieved from Meuuniere arrives at Zonnet Junction. Michael and his comrades witness its opening to reveal the first armor of the Original Seven, called the Saudade of Sunday.
Van and Wendy find themselves to a city inside a ravine ruled by identical twin sisters who hate each other. The twins fight to claim their deceased father's inheritance all for themselves. Carmen 99 meets up with Van and informs him that he can get information about The Claw if he becomes one side's bodyguard and does battle with another hired gun to determine the winner between the two sisters. Van is hired by Earl Driver, and another man named Ray Lundgren is hired by her sister Elle Driver. After a few initial hostilities, Van discovers that Ray, likewise, is hunting the Claw for exactly the same reason, but Ray's desire for revenge has turned him cold, heartless and determined to succeed at any cost whether it be to himself or others. During their supposed match, Ray steals the key of the inheritance, finding out that the father had used various twin test subjects for a dual piloted armor. The twins, having both gone rather insane, then take the armor. Realizing the deals gone south, Carmen 99 finds and takes two golden decorations set with large colored stones as compensation for her trouble, and escapes with Wendy leaving Van to take care of himself. Fearing the destruction the twin could wreak in their armor, Van summons Dann but tries reasoning with the twins first. Ray has no such compulsion, and after summoning his armor, he strikes decisively and violently destroying the armor with the twins still in it despite Van's interference. Van emerges from the smoking crater alone to rejoin Wendy and Carmen 99, who then takes off leaving the two of them to continue their trek across the desert.
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.
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.
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.
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.
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'.
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.
Claire has been demoted from working in Control Section to replacing Hachimaki in Debris Section. Hachimaki and Hakim encounter unexpected difficulties completing a 10-day group endurance test, the second round of testing for those wishing to join the Von Braun.
On Hachimaki and Tanabe's visit to the Moon, they meet Tanabe's neighbours... a group of wannabe ninjas who perform ninja techniques through the Moon's lower gravity.
As tensions rise among the crew over the point system, a new enemy comes forth from space.
Yuyama becomes an increasing threat to Nakaiya Juubei; Saigo Magozou is sent to assassinate him. Youjiro's history is revealed.
Juubei's death threatens to split the troupe apart.
The English knights launch a second attack, but it ends in disaster.