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.

Ordered to depart Hong Kong City, the Audhumla makes its preparations for departure. As the midnight deadline looms, Kamille and Four enjoy their last few hours together, but their romance is interrupted as Wooder launches a brutal attack on the city. Four returns to the Psyco Gundam's cockpit, and she and Kamille face each other in battle once again.

The former Mirai Yashima, now Bright Noa's wife, has brought her children to Hong Kong City in hopes of taking them into space. But her reunion with Amuro now puts her family in danger, as Wooder takes Mirai and her children hostage in an attempt to capture the Audhumla. Meanwhile, Kamille encounters Four in person, and the two enemies experience a powerful mutual attraction.

After crossing the Pacific, the Audhumla stops at Hong Kong City for resupply. But the rebels are still being pursued by Buran's forces, now commanded by his aide Ben Wooder. The Federation's Murasame Newtype Lab, responding to Wooder's request for reinforcements, dispatches the Cyber-Newtype Four Murasame and the immense Psyco Gundam to attack the city.

The Audhumla reaches Hickory and the Karaba members prepare to send Char and Kamille back to space. As Buran begins another attack on the rebels, Amuro enters combat to buy time for the shuttle launch. Kamille leaves the shuttle to help Amuro, and the former and current Gundam pilots find themselves fighting side by side to ensure that Char returns to space.

Karaba agent Beltorchika Irma arrives aboard the Audhumla to guide it to Hickory, and she is immediately fascinated by the famous Amuro Ray. But even though Amuro has regained his freedom, he still lacks the will to fight, and Katz is disappointed by his hero's hesitation. When the Audhumla is attacked by the Cyber-Newtype Rosamia Badam, Katz steals the Gundam Mark II and attempts to defeat the enemy himself.

Char and Kamille, left behind on Earth, join their Karaba allies aboard the transport plane Audhumla and set off for Karaba's Hickory base. Buran's forces continue their pursuit, with the help of reinforcements from the Federation's Newtype Labs. And Amuro Ray, the former war hero and Gundam pilot, escapes from his government caretakers with the help of young Katz Kobayashi and comes to join the rebel cause.

The AEUG pilots have escaped from Jaburo and joined forces with Hayato Kobayashi, a leader of the Karaba resistance group which fights the Titans on Earth. Hayato leads them to the Kennedy Spaceport, whose shuttles will send the AEUG pilots back to space. As the launch countdown begins, Char and Kamille struggle to protect their comrades from a Federation pursuit force led by Buran Blutarch.

The AEUG mobile suits descend to Jaburo and fight their way into the underground base, easily overcoming the unexpectedly light resistance of the Federation Forces. Inside the base, Kamille faces off against a vengeful Jerid and attempts to locate the captive Reccoa. Meanwhile, the AEUG pilots learn that they have walked into a lethal trap, and must now race against time to escape from Jaburo.

The Argama, now commanded by former White Base captain Bright Noa, joins the AEUG fleet to launch an orbital attack on the Federation Forces' Jaburo base. But as the AEUG mobile suits prepare to descend to Earth, the fleet suffers a surprise attack by Paptimus Scirocco, the pilot of the mysterious mobile armor that attacked Bright's shuttle. And as the AEUG forces enter the atmosphere, Jerid and his Titan comrades join the fray as well.

Having successfully captured several ships at Granada, the AEUG launches its new fleet to carry out the Jaburo operation. As the Argama leaves the moon, its crew see a space shuttle under attack by a mysterious mobile armor. Char and Kamille rescue the shuttle's passengers, and find a couple of familiar faces among them.

A mysterious mobile suit infiltrates the space colony known as Gryps, headquarters of the dreaded Titans. Its pilot is Char Aznable, the infamous Red Comet, who now fights for the rebel AEUG group under the alias Quattro Bajeena. After confirming that the Titans are developing a new Gundam mobile suit, Char rejoins his teammates at the civilian colony Green Noa 1, where more of the new Gundams are being tested, and signals the AEUG flagship to begin its attack.

The Argama and Radish descend into Earth orbit to collect Char as he returns from Earth, but the Alexandria is once again in hot pursuit. Yazan's mobile suit forces attack the AEUG warships, while Jerid, Mouar, and Sarah prepare a trap for the Zeta Gundam. As Char's shuttle arrives in orbit to rendezvous with the Argama, Sarah targets the Zeta with a powerful mega launcher.