It's the year AC (After Colony) 195. Over the past century, humanity has established a number of space colonies, giant wheel-shaped constructs that are home to millions of people. These colonies are grouped in clusters at the five Lagrange points, areas of relative stability in Earth orbit.
For decades, while the Earth's surface was wracked by war and civil strife, the peace and quiet of the space colonies presented an attractive alternative for war-weary settlers. When the terrestrial wars ended, a new world government was established, a "United Earth Sphere Alliance" committed to bringing about peace through force of arms. In the name of peace and justice, the Alliance seized control of the colonies.
To lobby the Earth's nations for autonomy, the space colonists chose a man named Heero Yuy as their representative. The charismatic Yuy united the colonies, and his message of demilitarization and non-violence was well-received by the people of Earth. But when Yuy was assassinated in the year AC 175, the colonists' hopes were crushed and the colonies thrown into turmoil.
Under the pretext of restoring order to the colonies, the Alliance staged a second military intervention, using humanoid fighting machines called mobile suits to crush all opposition. The colonies were placed under martial law, and all communication and cooperation between colonies was prohibited. Even terrestrial nations sympathetic to Heero Yuy's philosophies, like Europe's pacifist Sanc Kingdom, were crushed by the Alliance's overwhelming force.
Behind the scenes, the Alliance is being manipulated by the Romefeller Foundation, the powerful industrial combine that develops and manufactures its mobile suits. The Alliance's elite mobile suit corps, the "Specials," is trained and staffed by the Romefeller Foundation. In fact, the Specials are nothing but a front for OZ, a Romefeller subsidiary which has been recast as a secret society. Answerable only to the Romefeller Foundation, OZ has infiltrated the highest levels of the Alliance military.
After two decades of oppression, a network of rebels based in the space colonies decides to strike back at OZ and its puppet Alliance. Resistance groups at each of the five colony clusters work independently on their part of Operation Meteor, each retaining the services of one of the scientists who helped create the first mobile suits. Using the super-strong armor material Gundanium, the scientists construct advanced mobile suits called "Gundams," entrust them to five highly-trained, resourceful young pilots, and dispatch them to Earth to wage guerilla war against the Alliance.
Of the five Gundam pilots, the L5 colony cluster's Chang Wufei, L4's Quatre Raberba Winner, L3's Trowa Barton and L2's Duo Maxwell reach Earth without incident. But L1's Gundam pilot, a grim youth codenamed Heero Yuy after the martyred colonial leader, is intercepted by Specials ace pilot Zechs Merquise and forced to temporarily ditch his Gundam at sea. Staggering ashore, Heero encounters Relena Darlian, daughter of the Alliance's foreign minister. Heero promises to kill her to conceal his identity, but it soon becomes clear he can't bring himself to carry out the threat.
Terrified of the unstoppable Gundams, the Alliance generals send Relena's father to open negotations with the space colonies. Specials leader Treize Khushrenada is determined to thwart these peace overtures, and dispatches his trusted aide Lady Une to sabotage the diplomatic mission. Relena's father is assassinated by Lady Une and, with his dying breath, reveals Relena's true identity - she is Relena Peacecraft, princess of the Sanc Kingdom that was crushed by the Alliance thirteen years ago. What she doesn't yet know is that her long-lost brother Milliardo is in fact Specials ace Zechs Merquise.
The Alliance generals meet and decide to make peace with the colonies. When the Gundam pilots attack the meeting, cunning Treize evacuates the peace-minded generals in an OZ shuttle, making them irresistible targets. With the Alliance's leaders slain, OZ discards the "Specials" moniker and seizes power under its own name, launching Operation Daybreak to wipe out all resistance from the Alliance's terrestrial forces. The coup serves a more private purpose for Zechs, the erstwhile Milliardo Peacecraft, as he avenges his father's death by slaying the Alliance general who conquered the Sanc Kingdom.
With Earth under its complete control, OZ readies for the conquest of the space colonies. For this purpose the Romefeller Foundation has developed unmanned, computer-controlled mobile suits called "mobile dolls," faster and more lethal than any human pilot. Ordered to prevent these new weapons from being sent into space, the Gundam pilots find they've been lured into a trap when Lady Une orders them to surrender or witness the destruction of defenseless space colonies. Breaking off a duel with Zechs, Heero defiantly self-destructs his Gundam and buys enough time for Treize to overrule Lady Une's unsportsmanlike plan. The mobile dolls are delivered on schedule, as Trowa carries Heero's battered body to safety.
Compelled by honor, Zechs rebuilds Heero's ruined Gundam, then tracks down the wandering Gundam pilot and challenges him to a rematch at a remote Antarctic base. Zechs' activities do not escape the attention of the Romefeller Foundation, which dispatches a small army to the Antarctic to eliminate the rogue ace. Holding off the Foundation's hit squad, Zechs allows Heero and Trowa to escape.
The five Gundam pilots hijack shuttles and launch into space to defend their home colonies. But OZ uses its dreaded mobile dolls against the Alliance occupation forces, rather than the colonies themselves. After twenty years of the Alliance's tyranny, the colonies are easily persuaded to welcome OZ as a liberator. Submitting to OZ's benevolent guidance, the colonies begin arming themselves - thus funneling more money into the Romefeller Foundation's coffers - and brand the Gundam pilots who fought on the their behalf as troublemakers and subversives.
Manifesting an unexpected split personality, Lady Une becomes OZ's saintly emissary to the colonies. In her more familiar persona, she orders the capture of the five scientists who created the Gundams, and has them brought to OZ's lunar base to develop new mobile suits under her supervision. Infiltrating OZ's ranks, Trowa is teamed up with the captured Heero; the pair are put to work as test pilots to gather data on the new mobile suits.
In their first combat foray, Heero and Trowa intercept Zechs Merquise as he launches into Earth orbit. Claiming to be an ambassador from the non-existent Sanc Kingdom, Zechs has come to make a goodwill tour of the space colonies and urge them to reject OZ's militarism. While he begins his diplomatic tour, Duo and Wufei also attempt to attack OZ's lunar base and are captured in turn. All this is according to the plan of the five scientists, who have gathered all but one of their Gundam pilots while secretly using OZ's resources to rebuild Duo's and Wufei's ravaged Gundams. But one Gundam pilot remains unaccounted for...
Quatre has returned to his family's factory asteroid. Here, he sees his pacifist father's civilian employees pledge their allegiance to OZ, killing father Winner in the process. Temporarily unhinged by this traumatic experience, Quatre digs up the blueprints of the ancestor of all the Gundams - the never-completed, hideously destructive Wing Gundam Zero - and begins a one-man war against OZ. But the Wing Gundam Zero's brainwave control system turns out to have mind-warping side-effects. Sliding into madness under the "Zero System"'s influence, Quatre extrapolates his father's pacifism into a mandate to punish the colonies for subscribing to OZ's militarism.
Lady Une dispatches Heero and Trowa to stop Quatre's rampage. In the course of the battle, Trowa sacrifices himself to save Heero; Quatre is shocked back into sanity, and returns with Heero to OZ's lunar base. But while they were away, the political situation has taken a turn for the bizarre.
To protest the Romefeller Foundation's plans - in particular, its increasing use of mobile dolls, which he considers dishonorable - Treize resigns his position as OZ's leader. OZ promptly splits into two factions, one loyal to the Foundation and another following Treize. The Romefeller faction takes over OZ's lunar base. Lady Une is shot, but not before saving Duo, Wufei and the five scientists from termination at the Romefeller faction's hands. Heero and Quatre, finding themselves caught in the middle of OZ's civil war, abandon the madness-inducing Wing Gundam Zero and flee to Earth.
In order to eliminate the Treize faction, the Romefeller Foundation launches Operation Nova, a massive invasion of Earth using new mobile dolls based on the work of the five scientists. Zechs attempts to intercept the Foundation's forces, but he is just one man against legions.
On Earth, Heero and Quatre find their way to the Sanc Kingdom, resurrected under the leadership of Relena Peacecraft and dedicated to the principle of total pacifism. Accepting Relena's invitation, they soon find themselves busy fending off the Romefeller Foundation's incursions. They must also contend with the devious and conflict-loving Dorothy Catalonia, an "exchange student" from the Romefeller Foundation. Ostensibly there to study Relena's pacifist philosophies, Dorothy is actually the eyes and ears of her grandfather Duke Dermail, leader of the Romefeller Foundation.
The Foundation concludes Operation Nova with a massive assault on Treize's headquarters in Luxembourg. Heero arrives at Luxembourg just as Treize's forces collapse, and the former OZ leader gives him a dubious gift - the mysterious Gundam Epyon, equipped with its own Zero System. Meanwhile, in space, the Romefeller faction attempts to lure Zechs to his death by using the Wing Gundam Zero as bait. The trap fails, instead giving the rebel ace a sorely-needed hardware upgrade.
With the Treize faction defeated, the Romefeller Foundation turns its attention to the pacifistic Sanc Kingdom. Heero, Quatre and the other defenders fight fiercely, but Relena surrenders rather than see her kingdom turned to rubble. Heero, driven to a berserker frenzy by the Gundam Epyon's Zero System, fights on until Zechs arrives from space, too late to save his family's kingdom from a second conquest. Zechs and Heero duel each other until they collapse, trade Gundams, then gather their Zero System-addled wits and fight their way to freedom.
Now a captive of the Romefeller Foundation, Relena receives a surprising offer from Duke Dermail. To legitimize its conquest, the Foundation plans to declare the establishment of the "World Nation," and Queen Relena Peacecraft would make an excellent figurehead. Relena accepts, and then readies her address to the Romefeller Foundation's members. Amazingly, her appeal to the assembled executives - that, with total power now in their hands, they can afford to be magnanimous and strive for peace, justice and enlightened coexistence between Earth and the space colonies - is enthusiastically accepted. The Romefeller Foundation's members pledge to reject Dermail's empire-building and become good guys.
Just as the Romefeller Foundation dedicates itself to peace and justice, a new faction enters the fray. Masterminded by the wizened, enigmatic Quinze - the man behind Operation Meteor - rebellious OZ members and colonial resistance fighters form a militia group called "White Fang," dedicated to total independence for the space colonies. In short order White Fang occupies the lunar base, captures its mobile doll production facilities, and seizes the Foundation's ultimate weapon, the nearly-complete space fortress Libra.
Just as the Romefeller Foundation sought a figurehead, so too does White Fang. Quinze recruits Zechs Merquise as White Fang's token leader, and he proves to be just as difficult to control as his sister. In a worldwide broadcast, Zechs declares that, since Earth and the space colonies can never peacefully coexist, he will destroy Earth. As Zechs declares his intentions, the Romefeller Foundation's hapless Duke Dermail, attempting to reassert his leadership by personally leading an offensive to recapture Libra, is vaporized by White Fang's forces.
With the magnitude of the White Fang threat now apparent, the Romefeller Foundation's members are panic-stricken. Taking advantage of their abject terror, Treize stages a coup d'etat and seizes control of the World Nation. The deposed Relena leaves for space with the intention of talking some sense into her brother. Dorothy follows suit, with quite the opposite intention.
While all this frantic realignment is going on, Quatre and the Sanc Kingdom's other defenders have returned to space. They discover that Trowa is still alive, albeit temporarily amnesiac, and convince Duo to join their ranks.
Wufei, meanwhile, has seen his home colony destroyed and launched into a suicidal rampage. In the depths of his despair he encounters Heero, and the mind-warping effects of the Wing Gundam Zero's control system actually serve to straighten out his tormented mind and reveal the solution to the current crisis: Both Treize and Zechs must be eliminated for the sake of world peace. Soon all five Gundam pilots are gathered at the space fortress Peacemillion, ready to intervene in the escalating conflict.
As Treize begins fighting back against White Fang, Zechs employs his ultimate weapon, blasting Earth with Libra's powerful main gun despite Relena's attempted intervention. The Gundam Team attempt to fight their way through White Fang's legions of mobile dolls to Libra itself, but Zechs holds them back by adapting the Gundam Epyon's Zero System into a remote control system through which Dorothy can coordinate mass quantities of mobile dolls.
Treize gathers the entire forces of the World Nation for an all-out assault on Libra. Before sending his soldiers to their doom, he attempts to resolve the situation by challenging Zechs to a one-on-one duel, but the no longer honor-obsessed Zechs responds by blasting him with Libra's main gun. Though Treize is prepared to let Zechs kill him, the comatose Lady Une awakens just in time to race to the scene and shove Treize out of the way of the lethal beam. With no other option, Treize orders the World Nation into a hopeless battle against White Fang's hordes of mobile dolls.
As the battle rages, the Gundam Team's allies physically ram Libra with the space fortress Peacemillion. The collision destroys Libra's main gun, but since its engines are still intact, Zechs orders Quinze to set Libra in motion toward Earth and thus create an impact large enough to render the planet uninhabitable. Breaking into the damaged Libra, the Gundam Team destroy the mobile doll control system and locate the five scientists.
Treize is killed in mortal combat with Wufei, whereupon Lady Une promptly declares the surrender of the World Nation. But though the war is over, Zechs is still determined to carry out his threat to destroy Earth, and Libra's descent continues.
Now Zechs has one last loose end to attend to - his long-delayed showdown with Heero. The two rivals fight on and on throughout Libra's crumbling innards, while Lady Une has their pointless duel broadcast worldwide as a case study in the futility of war and hatred.
The five scientists attempt to use Peacemillion's engines to reverse Libra's course. Quinze, appearing too late to stop them, disappears along with the scientists in the explosion of Peacemillion's engines. Though the gambit is successful, a large fragment of Libra snaps off and continues its inexorable descent.
Now it's up to Heero. Dealing a crippling blow to Zechs' Gundam Epyon, he proceeds to the main engine of the remaining Libra fragment but discovers he's used up all his ammunition. Just as Heero is about to self-destruct in a desperate attempt to destroy the engine, Zechs appears and takes it out for him, promising they'll meet again as he's enveloped by the blast. As the falling hulk enters Earth's atmosphere, Heero recovers the Wing Gundam Zero's mighty rifle and demolishes the last fragment of Libra with one final, desperate shot.
With Zechs and Treize out of the picture, peace is indeed at hand. Representatives of the space colonies make peace with the World Nation, establishing the Earth Sphere Unified Nation. Relena and Lady Une take their places in the new world order and devote their energies to serving humanity, while the Gundam pilots quietly retire... for now.