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"A New Leader" Howard, an ally to both Duo and Zechs, agrees to team up with all the Gundam pilots and offers his ship, the Peacemillion, as a base. Relena announces that the Romefeller Foundation must disarm and calls for peaceful coexistence between Earth and colonies. Heero, in an attempt to kill her to end the false peace, spares her when he and Relena see the response Romefeller has given her is positive. Dermail is killed trying to regain power in space while White Fang's new leader, Milliardo Peacecraft, declares war on Earth.

"Trowa's Return to the Battlefield" Zechs accepts an offer from Quinze to become the leader of White Fang. While Dermail intends to continue using Relena as a figurehead, Dorothy and Marquis Weiridge conspire with other members of Romefeller to make Relena a queen in power as well as name. Meanwhile, White Fang's repeated advances convince Duo to leave Hilde's colony for her own protection. Trowa, Quatre, and Noin are mistaken as White Fang members by an OZ unit in the ruins of a nearby colony; after turning the tide of the resultant battle, Duo agrees to join the group.

"The Birth of Queen Relena" Informed by Duo, Quatre approaches Trowa and asks for forgiveness. As Quatre and Noin fight the new faction, White Fang, Trowa, despite the fact he still remembers nothing, agrees to fight with them in hopes of recovering his memory. Queen Relena eliminates all international boundaries and founds the World Nation in hopes of bringing peace.

"Zero VS Epyon" Zechs arrives in the Sanc Kingdom too late and is devastated - he (piloting the Wing Zero) ends up fighting Heero (piloting the Epyon), but the battle ends in another draw and they exchange Gundams before parting ways again. Relena reluctantly takes Duke Dermail's offer to become the new representative of Romefeller. Meanwhile, the Lunar Base and the uncompleted Libra are hijacked by the White Fang revolutionary army as they begin their quest to take back space from Romefeller, and Tsuborov is killed during Wufei's attack on the Lunar Base.

"Sanc Kingdom's Collapse" Duo finds Trowa alive and working at the circus, but realizes that Trowa has lost his memory and is soon driven away by Catherine. Relena is forced to dissolve the Sanc Kingdom in order to save the lives of the people in the country and agrees to become a prisoner of OZ, though Dermail realizes that she might be the symbol needed to unify OZ which Romefeller presently lacks. Noin and Quatre leave for space while Heero loses control of the Epyon and continues to destroy the mobile dolls.

"The Return of Wufei" Wufei returns to his home colony with his upgraded Gundam, but is forced to witness its destruction when they believe it is the only path to take against OZ. Zechs offers to become his ally and the use of the Wing Zero, but after being driven insane by the ZERO System, Wufei finds that Zechs lacks the justice to properly bring about peace. Quatre goes to the desert to retrieve his newly-rebuilt Gundam from the Maganac Corps. Meanwhile, Duke Dermail authorizes Tsuberov to begin construction of the fortress cannon Libra in hopes of using it as a symbol to unify the soldiers.

"And Its Name is Epyon" Heero enters Treize's Luxembourg mansion. There, a philosophical Treize presents Heero with the Gundam Epyon, which is equipped with the ZERO System just like the Wing Zero. Meanwhile, OZ's attempt to destroy the Wing Zero is intercepted by Zechs, who sacrifices the Tallgeese as a distraction in order to acquire the Gundam.

"The Lonely Battlefield" Relena meets with Duke Dermail, who declares the Sanc Kingdom hypocritical as Zechs continues to fight Romefeller in space. Meanwhile, when Treize's base in Luxembourg is under attack from an army of Virgos, Heero arrives with his Gundam to assist the Treize Faction. However, he soon finds himself overwhelmed by the continuous waves of mobile dolls.

"The God of Death Meets Zero" While working on salvaging the parts to complete his upgraded Gundam, Duo is captured and forced by Trant to test the ZERO System for OZ, but is driven nearly insane. He is rescued by Hilde as Trant attempts to master control of the Wing Zero. However, the ZERO System also drives Trant insane and he dies as a result of it.

"The Glass Kingdom" While Heero intends to take his Gundam back and leave, Quatre convinces him to stay in the Sanc Kingdom to defend Relena. Later, when OZ attacks a Treize Faction unit hiding in the Sanc Kingdom as an excuse to invade the pacifist nation, Heero leads a counterattack with the Wing Gundam and (once again) saves Relena's life in the process. Although she advocates pacifism, Relena allows Heero and Noin to form a small defense force of mobile suits to defend the country.

"The Reunion with Relena" Heero fights as a mercenary for the Treize Faction, while Quatre decides that after the battle he will go to the Sanc Kingdom. Noin arrives with the Wing Gundam's buster rifle to help even the odds and later brings the two pilots to the Sanc Kingdom, where Relena is waiting.

"The Heroine of the Battlefield" Sally is captured by OZ, but is able to hide Heero's Wing Gundam until Noin arrives and helps her recover it. Relena, now leader of the Sanc Kingdom, clashes ideals with Dorothy Catalonia, a new transfer student and granddaughter of Duke Dermail, who desires the thrill of war. Heero and Quatre, now back on Earth, escape from an OZ carrier.

"Passing Destinies" A recap episode from the point of view of Treize and Lady Une. At the conclusion of the episode, Treize's new creation is partly revealed: the Gundam Epyon.

"The Locus of Victory and Defeat" A recap episode from the point of view of Relena and Heero

The Eternal Flame of the Shooting Stars" Heero and Quatre are saved by members of the Treize Faction, consisting of soldiers still loyal to Treize, and meet the Gundam engineers. They explain that the Wing Gundam Zero uses a system known as ZERO, which increases skill but takes away free will, thus driving the pilot insane. They are captured again by OZ soldier Trant Clark, who forces Heero to test the ZERO System to gather data. However, this causes Heero to go on his own rampage with the Wing Zero inside the Lunar Base. Quatre manages to stop Heero before his insanity destroys them all, and the pair then escape to Earth.

"Quatre VS Heero" Heero fights Quatre in a near vain attempt to demonstrate that the colonies no longer need the Gundams, but when that fails, Trowa forces Quatre to realize his own kindness by paying the ultimate price. Meanwhile, the Romefeller Foundation proposes to replace all OZ mobile suits with their new Virgo mobile dolls and Treize is imprisoned when he refuses to support this. Lady Une, who learns of Tsuborov's treachery, is shot by Tsuborov when she unlocks Duo and Wufei's cell, allowing them to escape with their new, yet incomplete suits: the Gundam Deathscythe Hell and the Altron Gundam.

"The Gundam They Called Zero" Quatre, now mentally unstable, appears in the newly-constructed Wing Gundam Zero and begins to destroy various colonies one by one. Lady Une sends Heero and Trowa to fight back in the Mercurius and Vayeate, while Tsuborov, finding Une's behavior to be too lenient, stages a coup against her and cuts off the air supply to Wufei, Duo, and the Gundam engineers' cells.

"Duo, the God of Death Once Again" Duo and an OZ officer, Hilde Schbeiker, clash in ideals as to what will bring about peace, and she comes to his way of thinking. Duo, after running into the five engineers, allows them to turn him in if he gives them time to finish the construction of both his and Wufei's upgraded Gundams. Back on Earth, Sally manages to locate Heero's Wing Gundam (which he left behind).

"The Fight for Independence" Zechs, now going as Milliardo Peacecraft, meets with Lady Une as an ambassador of the Sanc Kingdom. When Nichol begins acting on his own, Une realizes that she's developed a split personality while trying to execute Treize's dream of the future and imprisons Nichol upon her return to Barge. Meanwhile, Wufei is captured by Chief Engineer Tsuborov of the Romefeller Foundation.

"Grief Stricken Quatre" Heero and Trowa confront Zechs for the first time since their battle in Antarctica and Zechs surrenders willingly. Quatre decides to build the original Gundam that the other five were based on after discovering files in the Winner family computer detailing its designs. Unwilling to compromise to OZ's ideals, Quatre's pacifist father evacuates their colony and sacrifices himself to destroy it before OZ can take advantage of it.

"The Lunar Base Infiltration" Sally infiltrates an OZ base in order to destroy the remains of Quatre's Gundam Sandrock, but the Maganac Corps convince her to allow them to take the pieces back to their base and rebuild it. Meanwhile, Duo's Gundam Deathscythe is destroyed in a public viewing of space by possible OZ recruits, one of whom is a familiar face. Heero sneaks into the Lunar Base in order to destroy the two new mobile suits, the Mercurius and the Vayeate, only to be caught by Trowa, now a member of OZ.

"Assault on Barge" Duo is easily defeated and captured by OZ due to his Gundam's lack of mobility in space after trying to fight off mobile dolls, computer-controlled mobile suits that require no pilot. Heero sees the battle on television and goes to find and kill Duo, but ends up rescuing him instead. While Lady Une advocates peace, Wufei attacks Space Fortress Barge, but like Duo, his Gundam is unsuited for space combat and he is forced to escape before Une's subordinate, Nichol, finishes him off.

"Tallgeese Destroyed" Zechs fights a heavy battle with the Tallgeese against Alliance mobile suits, while Lady Une forces the Gundam engineers to design and build mobiles suits superior to the Tallgeese and the Gundams under the threat of destroying a shuttle with Quatre inside.

"Betrayed by Home, Far Away" Lady Une has become a diplomat of OZ to the colonies and the colonies debate if they should accept OZ's proposal. Duo and Quatre attempt to catch the attention of the other three Gundam pilots, while Une captures the five engineers of the Gundams. The five pilots take off into space after Quatre self-detonates his Gundam.

"The Sorrowful Battle" Heero and Trowa arrive at Zechs' Antarctica base, where Heero is reunited with his rebuilt Gundam. However, Heero chooses to use Trowa's Gundam Heavyarms to duel Zechs instead, until Relena's arrival to stop the battle interrupts them again. During this, Noin reveals to Relena that Zechs is her brother, Milliardo Peacecraft. When OZ carriers arrive to arrest him, Zechs decides to surrender to them in order to allow Relena and Noin to escape while Trowa uses the Wing Gundam to pick up Heero and escape as well.