Episode 1: The Meteor the Girl Saw
After Colony 195. A faction of colonists sends five Gundams to Earth in a plot to rebel against the Federation. Relena sees the face of Heero, one of the Gundam pilots, and therefore he determines to kill her.
Episode 2: The Gundam Called God of Death
Heero, who has infiltrated Relena's school in order to kill her, attempts to destroy his Gundam, which has sunk to the bottom of the ocean. Zechs, piloting a Cancer, discovers the Gundam, but then Duo appears in his Deathscythe...
Episode 3: Five Gundams Confirmed
Duo leaps into action to free Heero from the Federation. Zechs arrives at the Corsica Base and receives from Walker the Tallgeese, a Mobile Suit that is a match for the Gundams.
Episode 4: The Nightmare at Victoria
Zechs, having transported the Tallgeese to Victoria Base, is reunited with his old school friend, Noin. But that evening, Wufei springs a surprise attack on the base, killing all of Noin's trainees.
Episode 5: Relena's Secret
Relena and Mr. Dorlian are returning to the Colonies, but they are entrapped in Lady Une's plot. Relena hears from her dying father the secret of her identity, and meets the mysterious scientist, Dr. J.
Episode 6: Party Night
Returning to Earth, Relena hears that Heero is transferring out of her school. Heero points a gun at Relena, for knowing too much, but when OZ attacks he ends up protecting her.
Episode 7: The Scenario Leading to Bloodshed
Treize, the commander of OZ, skillfully manipulates information to lure the Gundams to the military reduction meeting. Caught in his trap, Heero mistakenly kills the pacifist General Noventa. As a result of this assassination, OZ is able to step onto the center stage of history.
Episode 8: Treize's Assassination
Heero, knowing about Treize's plot, is unable to hide his unrest. OZ determines to destroy the Gundams and their bases. Wufei, pursuing Treize, fights a duel with him and loses.
Episode 9: Portrait of a Ruined Country
The completed Tallgeese is delivered to Zechs. But he is severely injured trying to pilot it, since it is built without regard to human limitations. He is able to fulfill his mission with the self-sacrifice of his subordinate, Otto, and stands before his father's portrait swearing his resolve.
Episode 10: Heero, Blown to Bits
OZ, using the transportation of Tauruses as a decoy, plans the destruction of the Gundams. Zechs wishes to fight a duel with the Wing, but Lady Une threatens to fire on the colonies. There is nothing for Heero to do but self-destruct.
Episode 11: Where Has Happiness Gone?
With the colonies held hostage, the boys have no means to fight. Meanwhile, Relena, in her pursuit of Heero, meets up with Lady Une in Moscow. She attempts to kill her in revenge for her father's death, but fails. Noin gets Relena safely away.
Episode 12: Fighters Lost in Confusion
Heero, having been rescued by Trowa, regains consciousness after a month. Wufei, who has met Sally, is inspired by her actions to try fighting again. Meanwhile, Trowa decides on what he believes will be his final battle.
Episode 13: The Tears of Catherine
OZ begins to unfold its strategy of sweeping away the remnants of the Federation. Zechs puts himself under the command of the cruel young officers Alex and Muller. Meanwhile, Trowa has resolved to blow himself up in his final battle, but Catherine prevents him.
Episode 14: The Order to Blow Up 01
Relena, who is under the protection of Noin, faces members of the Romafeller Foundation and criticizes them. Heero, accompanied by Trowa, sets out on a journey to expiate his crimes. Zechs, deceiving the investigative group, brings the Wing back to life.
Episode 15: To the Battle at the South Pole
Heero and Trowa, having visited Mrs. Noventa, are invited by Noin to the South Pole, where Zechs is waiting. But they are followed by the shadow of the investigative group. Meanwhile, Relena, now aware that Heero is alive, hurries to the South Pole.
Episode 16: Sorrowful Battle
Heero arrives at the South Pole to find the repaired Wing waiting for him, as well as Zechs, who desires a duel. After an endless struggle, their fight is broken up by the arrival of Relena and the attack of a large enemy force.
Episode 17: Betrayed By the Distant Homelands
Lady Une, under orders from Treize, goes into space to work for peace. Meanwhile, Duo and Quatre decide to return to space as well, and launch a surprise attack on the spaceport. However, the colonies declare that they don't support the actions of the Gundams.
Episode 18: Tallgeese Destroyed
Lady Une captures the Gundam designers and forces them to build an even stronger Mobile Suit. Zechs, having surrendered to the investigative group, desires to die a heroic death for Treize. But Treize himself begins to question the Romafeller Foundation.
Episode 19: The Attack on Baruji
Duo, having returned to space, is captured during a battle with OZ. Heero, worried that OZ will use Duo, sets off to kill him. Meanwhile, Zechs, who was rescued by Howard, accepts his request to go into space.
Episode 20: Infiltration of the Moon Base
While Lady Une is proposing independence at the colony assembly, the new model Mobile Suit is being completed. Heero, aware of this, goes alone to infiltrate the Moon Base, but ends up surrendering to Trowa.
Episode 21: Sorrowful Quatre
Lady Une, having information that Tallgeese has entered space, orders Heero and Trowa to shoot it down. Meanwhile, Quatre returns to his dear homeland. But the inhabitants have been won over by OZ and kill Quatre's father when he refuses to go along with them.
Episode 22: The Fight to Bring Back Independence
Mirialdo, entering space as a friendly ambassador, receives a courtesy call from Lady Une. Treize tells Lady Une he is not going into space, and, while she is torn, she decides that it will be best for her and Treize's future, to fight.
Episode 23: Duo Returns to Shinigami
The colonies, manipulated by OZ, are beginning to build up arms. Meanwhile, Duo had plotted to infiltrate the Moon Base to destroy the assembly-line production of Mobile Suits, but is prevented by Hilde, an aspiring soldier.
Episode 24: The Gundam Called Zero
While four of the boys are at the Moon Base, a resource satellite is destroyed by a mysterious Mobile Suit. Trowa realizes it is Quatre's Mobile Suit, but Quatre, whose heart has been shattered, attacks his friend.
Episode 25: Quatre vs. Heero
Heero, standing up against the out-of-control Quatre, suffers under the power of the Zero. Trowa sacrifices himself in order to snap Quatre out of his insanity. Treize disagrees with the Romafeller Foundation, which envisions an easy rule, and steps down as commander of OZ.
Episode 26: The Meteor That Doesn't Burn Out
The Romafeller Foundation, having space firmly in its grasp, sends battalions of Mobile Dolls down to Earth. Soldiers loyal to Treize continue to rebel and stir up dissension within the ranks. Meanwhile, Heero, still a prisoner, loses control in the Zero System cockpit. He goes to face Quatre.
Episode 27: Where Victory and Glory Are
While Heero and the others fight in space, Relena makes efforts to revive her homeland. She recalls all that has happened since the day she saw the meteor. She continues to wait for Heero.
Episode 28: Different Fates
Treize, having resigned as commander, is held in confinement at the headquarters of the Romafeller Foundation, where he thinks over his own actions. Pondering the five boys with their new value, so different from his own ideals, Treize undertakes the development of a new Gundam.
Episode 29: Heroine of the Battlefield
Relena, having revived the Sank Kingdom, sets it on a path of complete pacifism. Then Dorothy arrives on the scene, a girl with Romafeller blood, who looks forward to war.
Episode 30: Reunited with Relena
Quatre, questioning Heero, who is fighting as a hired soldier for Treize's faction, hears from some pacifists about Sank Kingdom. He believes it is his mission to defend such a peaceful way of life, and journeys there with Heero.
Episode 31: The Glass Sank Kingdom
Arriving in Sank Kingdom, Heero and Quatre enroll in Relena's school and began student life there. But the Romafeller Foundation, unfriendly to pacifism, begins a well- orchestrated attack, and the boys fight back to protect Relena.
Episode 32: The Battle Between Shinigami and Zero
Duo, who remained in space, was planning a guerrilla attack. But before he can begin, Trant appears, a man who seeks to gain comprehensive knowledge of the Zero System. Duo, in the Zero, fights a desperate battle, and finally destroys Trant.
Episode 33: Battlefield of Solitude
Zechs, once again wearing his mask, challenges the Romafeller Foundation. Dermail realizes that he is really Milliard Peacecraft, and summons Relena for cross-examination. Meanwhile, Heero sets off for an even more dangerous battlefield.
Episode 34: Its Name is Epyon
Zechs, having taken possession of the Zero, attacks the Mobile Dolls during their descent. Heero infiltrates the base at Luxembourg, where Treize entrusts him with the Gundam Epyon.
Episode 35: Wufei Once Again
Wufei, chosen once again to be a Gundam pilot, witnesses the resolution of his people as they blow themselves up when they are attacked by the enemy. Zechs wants to obtain the cooperation of the Gundam pilots, and contacts Wufei, but meets with a forceful rejection.
Episode 36: The Collapse of Sank Kingdom
The Foundation at last begins the conquest of the Sank Kingdom. Quatre and Noin fight along with the Maganac fighters to defend it, but Relena puts a stop to what she feels is a stupid fight, and the Kingdom surrenders to the Foundation.
Episode 37: Zero vs. Epyon
The Sank Kingdom falls with Relena's surrender. But Heero, under the influence of the Zero System, goes ahead and fights with Zechs. Meanwhile, Relena has been taken to Romafeller Foundation headquarters, where she is installed as their representative.
Episode 38: Relena Becomes Queen
While the armed group White Fang are revolting in space, Noin and Quatre also go into space, searching for the other Gundam pilots. Meanwhile, the Foundation, recognizing the power of Relena's influence, supports her as universal queen.
Episode 39: Trowa Returns to the Battlefield
Relena, having become the Foundation representative, infiltrates the minds of the core members with her ideas of absolute pacifism. The White Fang leader, Quinze, approaches Zechs, asking for his participation. And Heero begins to act on his plans to assassinate Relena.
Episode 40: A New Leader
Four of the boys gather in space on the Peacemillion. The other boy, Heero, plots to assassinate Relena, but decides to give her ideals a chance. However, Zechs declares that space and the Earth are separate and denies her authority.
Episode 41: The Battle Over Baruji
The battle over Baruji, which will decide supremacy in space, begins. Treize takes the place of the agonizing Relena, and takes into his hands the real power of the Foundation. In space, Zechs, without giving Noin a satisfying answer, attacks and takes down Baruji.
Episode 42: Libra Set in Motion
The unconscious Lady Une is returned to Treize, who is preparing for war. Meanwhile, Wufei, seeking a decisive battle, is shown the path he should take by the Zero System. Zechs orders the Libra in the direction of the Earth.
Episode 43: The Aurora Bombarding the Ground
While Heero and the others come together on the Peacemillion, remnants of OZ occupy the colony where Catherine is. Trowa sets off alone in the Zero to rescue her. Due to the influence of the Zero System and the efforts of Quatre, his memory is fully restored.
Episode 44: The Gundam Team Launches its Attack
Relena boards the Libra, seeking to ascertain her brother's true intentions, but their views will never meet. Meanwhile, Quatre is made to operate the Zero System for the good of space.
Episode 45: Premonition of Battle
Hilde steals data from the Libra and escapes. After her come the Mobile Dolls with Heero and Trowa's fighting data imprinted in their systems. Duo sets off in the midst of battle to rescue her, and destroys the two Mobile Dolls. She gives him the data.
Episode 46: Mirialdo's Decision
Heero learns from Hilde that Relena is on the Libra, and infiltrates it to hear Zechs' true intentions. Treize claims a duel with Zechs. He refuses, and presses the switch of the main weapon.
Episode 47: Space Clash
The armies of Zechs and Treize clash in the area of space around MO-II. The boys, seeing the main weapon of the Libra as a threat, attack Zechs. The Peacemillion crashes into the moving Libra, rendering it's main weapon nonoperational.
Episode 48: Attack into Chaos
Heero challenges Zechs to battle as Zechs attempts to crash the two interlocked warships down on the Earth. Meanwhile, Wufei tries to finish his duel with Treize. But Treize awaits his own death, thinking it will become a foundation for peace.
Episode 49: The Final Victors
With Treize's death, the World Nation Army accepts its defeat. But Zechs still wants to show the inhabitants of Earth the horror of war. Heero goes up against Zechs because only by defeating him will the war be finished. Meanwhile, in order to stop the warships from crashing, the scientists board the Peacemillion and disappear with Quinze in an explosion of light. However, huge fragments are still falling towards Earth. Heero destroys Zechs and prepares to use the only method left to him to stop the fragments. But Zechs uses the last of his strength to destroy most of them. Heero blows away the final fragment and his mission is accomplished. On this day, the Earth and space both embrace absolute pacifism.