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.

After the failure of Jamaican's colony drop, the ferocious Titan pilot Yazan Gable launches his own attack on the AEUG. As Emma and Katz battle Yazan's forces, they stumble across the wreckage of one of the Principality of Zeon's old battleships, which becomes the scene of a duel between Yazan and Kamille. His mobile suit damaged, Yazan retreats to the Alexandria, but he has one more surprise in store.

The AEU and the Union seem to have reconciled themselves to the existence of Celestial Being, but the Human Reform League is still determined to eliminate it. The Human Reform League launches an operation to track down the Celestial Being mothership Ptolemaios. Sergei Smirnov and his Chobu special forces team deploy huge numbers of tiny probes in Earth orbit. Sergei and Sumeragi match wits in a series of tactical feints, and Sumeragi realizes too late that the enemy's true objective.

An international terror network has begun a campaign of bombing attacks in order to force Celestial Being to halt its armed interventions. Princess Marina's diplomatic tour has now brought her to Scotland, where she encounters Setsuna in the aftermath of another terror attack. Meanwhile, the AEU and Union intelligence agencies provide Celestial Being with information on the terror network, allowing the Gundam Meisters to go into action against the terrorists.

Setsuna has been reunited with a figure from his past. His opponent is the mercenary soldier Ali al-Saachez, the same man who once trained Setsuna as a child soldier. The Gundam Meisters force the Moralian forces to surrender. Celestial Being tactical forecaster Sumeragi Lee Noriega is troubled by the knowledge that this mission has cost hundreds of lives, and more are soon lost as a worldwide series of terror attacks begins in response to Celestial Being's activities.

Celestial Being's activities have reduced the level of conflict in the world, but there are some who do not welcome this change. Among them is the southern European nation of Moralia. The AEU decides to hold a joint military exercise with Moralia as a show of support. Celestial Being prepares to intervene in this joint exercise. As the Gundam Meisters go into battle against a combined AEU, Moralia, and PMC force of more than a hundred mobile suits, Setsuna encounters a familiar adversary.

Kinue's younger brother Saji and fellow student Louise travel into space for a study tour. The Human Reform League begins a performance test of the Tieren Taozi, an experimental mobile suit designed exclusively for super soldier Soma. Allelujah is sent to observe the test, but he and Soma react strangely to each other's presence. When Soma loses control and opens fire on the nearby low orbital station, Saji and Louise find themselves in deadly danger.

The Human Reform League holds a memorial service for their dead. Sergei is put in command of a new team whose mission is to eliminate the Gundams. The team's trump card is a young woman, Soma Peries, Super Soldier Number 1. An international crisis begins as the South American nation of Taribia declares its independence from the Union. In the Kingdom of Azadistan, Princess Royal Marina Ismail anxiously watches the crisis unfold. The fate of her homeland may depend on how Celestial Being responds.

Union ace pilot Graham Aker learns that he and Billy Katagiri have been reassigned to a new anti-Gundam investigative taskforce. News reporter Kinue Crossroad discovers Celestial Being's spokesman is the legendary inventor Aeolia Schenberg... a man who died more than 200 years earlier. Setsuna is sent to eliminate the remaining Human Reform League forces on the island of Ceylon. Here he encounters another formidable new opponent: veteran officer Sergei Smirnov, the dreaded Wild Bear of Russia.

As the world reacts with confusion to Celestial Being's announcement, the Gundam Meisters prepare for a second mission. While Allelujah and Tieria descend from space, Setsuna and Lockon make contact with the Celestial Being agent Wang Liu-Mei, and all four Gundam Meisters then join forces for an armed intervention on the island of Ceylon.

Amuro lets petty annoyances get to him, and refuses to fight. Bright tries to rally Amuro, but it only incites him to rebel even more, and ends in a great argument. However, upon hearing Bright invoke the name of Char, Amuro decides to sortie, and uses the Gundam to display his astonishing tactics.

Some of the refugees have petitioned to be dropped off on the ground. Bright uses this as an excuse to ask the Zeon forces for a temporary cease-fire. The Gunperry transporting the refugees also secretly unloads Amuro's Gundam. Kai Shiden's Guncannon then descends to the ground to lure the enemy. The Gundam attacks from the rear of the lake with a pincer movement, and Bright's brilliant strategy unfolds.

By launching a Core Fighter into a ballistic orbit and having it fly over the enemy, the White Base tries to establish direct contact with Earth Federation Forces headquarters. Meanwhile, the refugees incite a revolt, but Amuro focuses on what he must do and heads to the hangar. Char senses the Core Fighter speeding away and intercepts it with a Komusai, but...

The White Base, having entered Earth's atmosphere, is attacked by the youngest member of the Zabi family, Garma Zabi, who commands a Gaw attack carrier and a formation of Dopp fighters. On top of this, Magella Attack tanks begin shelling from the ground. Bright has Amuro switch from the Guntank to the Gundam, and plots how to escape from the enemy's clever trap...