In an effort to end many years of tyrannical rule, five pilots and their Gundams are dispatched to Earth to begin Operation Meteor. Four land without incident, but one is intercepted and his mission is compromised.

Heero is injured and is kept for treatment at the Alliance hospital. At the Corsican base of the Mediterranean, the Gundam Heavyarms, piloted by L3's Trowa Barton, annihilates everything in its path. Then things get even worse for the Alliance when the Gundam Sandrock shows up.

Relena and her father, Vice Foreign Minister Darlian, journey to the colonies to try and prevent war. but there are those who do not want peace. Amidst the grief and tragedy, Relena learns her true identity...

Relena goes back to Earth. Wufei attacks another Alliance base and Trowa has started to work in a circus as a cover. Back at school, Relena tells Heero that she knows everything about him and invites him to a party, to be held that night.

Treize Kushrenada's plans to destroy the Alliance come to a head when the leaders of the Alliance hold a meeting. The meeting is led by Marshal Noventa and outlines his peace agenda. However, based on Treize's false intelligence, the Gundams destroy the Alliance leadership, and Oz begins to take over Earth.

The United Earth Sphere Alliance collapses, sending the entire Planet into a panic. This allows OZ to step forward and take control through a well planned coup. Zechs is occupied with other things: he is searching for the ruins of the Sanc Kingdom.

Lady Une briefs her troops on another strategy to try and wipe out the Gundams. Heero and Zechs face each other again, but this time it's the Wing Gundam versus the Tallgeese.

The Gundams must fight to regain peace. Wufei meets Sally Po on the battlefield and tells her that the weak should not be fighting. Still, lost in his emotion, Wufei once again gets into his Shenlong Gundam.

To try and make up for his mistake of killing the honorable pacifist leader Noventa, Heero confronts his granddaughter, Sylvia Noventa. Meanwhile, Zechs is handed an order from the Romefeller Foundation...

The Gundam Deathscythe single-handedly battles OZ's Mobile Suits in space, and Duo ends up getting captured. Heero searches for Duo in order to silence him...

OZ is developing 2 new Mobile Suits that can challenge the Gundams. Heero accepts the mission to sneak in and sabotage their operations. But he is unprepared for who he meets while inside the base...

A wild Mobile Suit approaches the colonies at high speed; Lady Une orders test pilots Heero and Trowa to stop it. Meanwhile, Quatre, exhausted from the pressure of his missions, returns home for a visit. But what he finds there is not comfort, only more chaos and tragedy.

The colonies have begun arming themselves for the coming fight against OZ. However, more surprising than that is the switch in Lady Une-she's become an advocate for peace. She is now acting on Treize's behalf without the consent of the Romefeller Foundation.

Trowa and Heero must battle their crazed friend; but they find themselves losing against this new Gundam. Treize, meanwhile, disapproves of the Romefeller Foundation's plan to use Mobile Dolls-automated Mobile Suits without pilots. His dissension results in his arrest by OZ.

Treize, while not in the middle of the battlefield, continues to scheme.

Romefeller is gaining ground on Earth very quickly and Treize and his troops seem to be losing the battle. When Heero realizes that Treize is now fighting Romefeller, he joins his army as a mercenary and finds himself working alongside Sally Po and Lucrezia Noin.

Quatre isn't convinced that Heero's mercenary path is the correct one. However, having witnessed the horrors of war, he cannot stand by and do nothing. When Relena declares the Sanc Kingdom's neutrality, Quatre and Heero take refuge.

Heero and Quatre decide to stay in the Sanc Kingdom and help Relena promote pacifism. But when the Romefeller Foundation attacks, Heero, Quatre and Noin go into battle.

Duo and Trowa are reunited and team up against the enemy once more. Meanwhile, the Romefeller Foundation has mounted a final assault against the Sanc Kingdom, forcing Relena to surrender to prevent a battle.

A group of rebel colony citizens calling themselves the "White Fang" starts attacking OZ bases. Quatre and Noin search for the other Gundam pilots. The Romefeller Foundation names Queen Relena as their representative.

As Relena takes her first step towards trying to achieve true peace, Heero sets out to eliminate her. Milliardo Peacecraft, the new leader of the White Fang, is now intent on going to war against OZ, the Romefeller Foundation and the Gundam pilots.

With Milliardo Peacecraft's declaration of war against the Earth in effect, the battle rages on between the White Fang and OZ. Meanwhile, Treize returns to take control of the Romefeller Foundation, forcing Relena to step down. In space, the Gundam pilots encounter Milliardo and his Epyon.

The survivors of the destruction of Barge are brought to Earth, one of them being Lady Une. Treize reveals his true intentions. As the battle continues, Relena heads for Libra.

The Gundam pilots reunite. OZ takes control of a colony demanding the White Fang surrender Libra. When Trowa learns that Catherine is in the colony, he leaps to action. Meanwhile, Relena struggles to talk some sense into her brother.

Heero plans to destroy the Wing Gundam before it is discovered by the Alliance forces. Heero gets his hands on two torpedoes and attempts to destroy his Gundam. Relena, refusing to believe Heero's threat, tries to confront him but is interrupted by the arrival of Duo Maxwell...