The Argama docks at Side 2's Colony 13, a neutral sightseeing colony, for another round of repairs. Kamille and Fa enter the colony to enjoy some leisure time, only to encounter a young woman named Rosammy who insists that Kamille is her long-lost brother, as well as a vacationing Mineva Zabi. Char discovers that the Titans have stationed snipers inside the colony's agricultural modules, and the ensuing fighting soon spills over into the colony itself.

Char and Kamille launch into orbit aboard a space shuttle to rejoin the Argama. They arrive to find the Argama under attack by the Alexandria and its mobile suits. Char targets the enemy ship with his mega bazooka launcher, but the Alexandria withdraws from the firing line just in time. Kamille senses a familiar presence aboard the Alexandria, but he can't bring himself to believe that Reccoa is still alive.

Char and Kamille travel with their Karaba allies to the Earth Federation capital at Dakar. Here they take control of the Federation assembly so that Char can deliver a speech denouncing the evils of the Titans. Jerid and his comrades attempt to destroy Dakar's communications center in order to stop the broadcast, but their actions serve to turn both the politicians and the public against the Titans.

Returning alone to the Kilimanjaro base, Kamille is finally reunited with Four Murasame. But Kamille's old enemy Jerid Messa is also at the base, and when he recognizes Kamille the pair are forced to flee for their lives. The Karaba forces resume their attack, and Four undergoes a dramatic personality shift, turning before Kamille's eyes into an emotionless fighting machine. As Kamille struggles to reason with her, Jerid intervenes with tragic results.

The AEUG's Karaba allies are staging an assault on a Titan base at Mount Kilimanjaro. The Argama descends into satellite orbit to support the operation, and Char and Kamille accidentally fall into Earth's atmosphere and find themselves in the middle of the battle. Kamille is astonished to see the Psyco Gundam enter the fray, and when he and Char infiltrate the Kilimanjaro base, they discover that its pilot Four Murasame is very much alive.

Despite the Argama's desperate need for repairs, the AEUG ships are ordered to continue their pursuit of the Gwadan and Dogosse Gier. Meanwhile, Reccoa is recovering from the injury she sustained while protecting Char, but she is frustrated by his callous attitude. When Yazan Gable launches an attack on the AEUG ships, Reccoa ignores Char's warnings and joins the battle, convinced that somebody is calling to her from the darkness of space.

Bright, Char, and Kamille join an AEUG delegation to the Axis warship Gwadan. Here they meet Mineva Lao Zabi, the child leader of the Axis forces. Char is outraged to discover that Mineva is being used as a puppet by her regent Haman Karn, and the negotiations quickly collapse. As the AEUG members make their escape from the Gwadan, Paptimus Scirocco sees an opportunity to establish his own alliance with Axis.

Forced to leave Von Braun City before completing its repairs, the Argama sets off on its diplomatic mission, only to find that the Titan flagship Dogosse Gier is also on its way to meet the Axis forces. With the AEUG's sponsors determined to contact Axis first, Char and Reccoa attempt a daring preemptive strike on the enemy ship. As the fighting intensifies, a new power enters the battlefield.

The asteroid Axis and its army of Zeon renegades are returning to the Earth Sphere, and the AEUG hopes to enlist their help in the struggle against the Titans. Before contacting the Axis forces, the Argama docks at the lunar city of Von Braun for repair and resupply. But when Kamille runs into Sarah Zabiarov in Von Braun City, he learns that the Argama is in deadly danger from the bomb she has planted at the city's spaceport.

In an attempt to destroy the Argama, the Alexandria uses Yazan's forces to drive the AEUG warship into a ruined space colony, where Jerid and Mouar are waiting in ambush. Kamille rushes back to protect the Argama and begins a fierce duel with Jerid. But Mouar, who has sworn to protect her partner, won't let him fall before the power of the Zeta Gundam.

Char and Kamille return to the AEUG flagship Argama with the captured Gundams. Meanwhile, the Titans dispatch the warship Alexandria, as well as reinforcements from the regular Federation Forces, to pursue the rebels. Titan pilot Emma Sheen is sent to the Argama to deliver a message from her commander Bask Om, but she is as shocked as the AEUG when the nature of Bask's ultimatum is revealed.

The Titans launch a new offensive against the space colonies of Side 2, where the AEUG enjoys strong support. Side 2's civilian leaders attempt to surrender, but the Titans are intent on carrying out a poison gas attack to teach the rebellious colonies a lesson, and the Argama and its mobile suits are the only ones who can save millions of innocent people from being massacred at the Titans' hands.

After the completion of Operation Apollo, Paptimus Scirocco has returned to his own ship, the interplanetary helium carrier Jupitris. The AEUG sends Reccoa to infiltrate the ship and gather information, with Kamille following in the Zeta Gundam to provide backup. While Reccoa boards the Jupitris and meets the mysterious Scirocco in person, Sarah Zabiarov spots Kamille waiting outside and engages him in combat.

Titan officer Jamaican Daninghan plans to drop an abandoned space colony onto the lunar city of Granada, one of the AEUG's main strongholds. However, his rival Scirocco sends Sarah Zabiarov to warn the AEUG, and the Argama rushes to stop the colony drop. Sarah, now a captive aboard the Argama, plays a cruel trick on the young AEUG member Katz Kobayashi in order to make her escape.

Kamille sneaks into the occupied Von Braun City to gather intelligence, only to run into Jerid and Mouar. As the AEUG forces attempt to recapture the city from the Titans, the fighting spreads into Von Braun's interior, and Kamille and his enemies take refuge inside the city's shelters. Meanwhile, Char travels to Earth with AEUG leader Blex Forer to attend a meeting of the Federation Assembly, with tragic results.

The Titans launch Operation Apollo, whose goal is the capture of the lunar city of Von Braun, and Scirocco dispatches Jerid to divert the AEUG's attention while the Titan fleet begins its attack. The AEUG pilots fight valiantly but are unable to stop the Dogosse Gier from breaking through into Von Braun's airspace, and they sense the power of Scirocco's presence as the Titan flagship descends into the city.

Jerid is assigned to lead a pair of Titan pilot cadets on a training flight. When he discovers Reccoa Londe transporting new machines to the Argama, he impulsively launches an attack. As Kamille comes to the rescue in his new Zeta Gundam, and Titan cadet Sarah Zabiarov experiences the terror of combat for the first time, Scirocco quietly observes the battle from the bridge of the Dogosse Gier.

Kamille returns to space and rejoins the Argama crew, but his experiences on Earth have left him shaken and heartsick. Meanwhile, the enigmatic Paptimus Scirocco joins forces with the Titans and is placed in command of their flagship Dogosse Gier. Also under Scirocco's command are Jerid Messa and his new partner Mouar Pharaoh, and Kamille finds himself in deadly peril when Jerid and Mouar attack with their powerful new transformable mobile suits.

The Audhumla resumes its journey and sets off to attack the Titans' New Guinea base. Desperate to stop the rebels, Wooder once again dispatches Four and the Psyco Gundam, and prepares to ram his own transport plane into the Audhumla. In the midst of battle, Kamille makes one last attempt to reach Four and tell her of his true feelings.

Char's team breaks into Green Noa 1 and begins a running battle with Federation Forces mobile suits. During the confusion, a young civilian named Kamille Bidan escapes from the Titans' custody and commandeers one of the new Gundam Mark II units. Out of hatred for the Titans, Kamille helps the AEUG capture a second Gundam and then joins the rebels in their escape from Green Noa 1.