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 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...

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.

L5's Wufei Chang, in his Shenlong Gundam, attacks the Taurus MS's transports after coming into Lake Victoria base late at night. Lucrezia Noin, head instructor at the base and good friend of Zechs Merquise, tries to fight him off in her Aries MS.

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.

Lady Une makes the Gundams her next target and activates the self-destruct sequence on the New Edwards Base. Can Heero prevent the explosion of the New Edwards Base and find the person who set them up? Meanwhile, Wufei duels with Treize.

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 have been defeated. With the colonies used as shields, the pilots don't have a chance. No one knows whether Heero is dead or alive. On the trail of her father's killer, Relena heads to Moscow. Duo and Quatre take refuge with the Maguanac Corps.

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.

Two misguided OZ soldiers are going on an execution spree, destroying any remaining Alliance resistance. In an effort to save the colonies, Trowa heads for his final battle. However, Catherine stands between him and his death wish...

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...

Zechs' warrior nature craves a decisive battle. Noin invites Heero to Antarctica, where Zechs awaits. Suspecting that Zechs has violated the order to destroy Zero One, the Romefeller Foundation sends troops after him.

At the South Pole, Zechs waits with the newly-rebuilt Wing Gundam. After Herro arrives and the rematch begins, Relena arrives and tries to stop them from wasting their lives. However, she discovers a revelation...

OZ sets in motion its plans to destroy the Alliance military once and for all. Quatre and Duo head to outer space to warn the colonies of the impending danger, only to discover they've been declared the enemy.

The fight between the Tallgeese and the Gundams conclude. Now, Zechs refuses to fight for, and ends his affiliation with 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.

With Lady Une's help, Duo escapes from OZ and goes to destroy the Mobile Suit production base on the moon. But while there, he meets a girl named Hilde who has become a soldier. The choice is suddenly much more complicated.

A Mobile Suit with fantastic power is on a rampage. It's attacking the colonies one after another in a brutal display of raw power. Trowa and Heero move to intercept this strange new Mobile Suit and are surprised by who its pilot is...

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 is freed by OZ soldiers loyal to him, but the trouble is only beginning. Romefeller is out to eliminate the Gundams and Treize, since they are symbols of hipe. Operation NOVA commences, and all of the Earth is in danger.

Relena, thinking back on past events, becomes determined to put an end to the Romefeller Foundation's tyranny.

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.