Senior Engineer Erica Simmons of Morgenroete reviews the Strike's combat logs and theorizes that Kira might be superior than any other Coordinator and speculates on the "SEED factor" theory. She shows Kira the mobile suits that Orb is developing and asks him to develop a mobile suit operating system that can be used by Naturals.

Kira and his friends are given the chance to meet with their parents who have taken refuge in Orb. Kira refuses to go, but his parents meet with Uzumi Nara Athha who hints there is a deeper connection between Kira and Cagalli. Kira instead completes the operating system for the Orb Union's MBF-M1 Astrays. When Kira's mechanical bird flies off, Kira finds himself standing face to face with Athrun. They part ways pretending not to know each other, but not without saying kind words about each other.

The Archangel, without Cagalli and Ledonir on board, leaves Orb territory for Alaska. The Zala Team, who is patiently waiting, engages them in a battle. Kira grounds the Duel, Buster, and Blitz with the help of Mu and Tolle, who is now the second Skygrasper pilot. As Kira and Athrun fight, Nicol intervenes, but he steps into Kira's fatal attack.

The Zala Team make another effort to destroy the Archangel and the Strike. Dearka in the Buster is shot down by Mu and surrenders. Tolle attempts to aid Kira, but he is killed by Athrun. The grief Kira and Athrun suffer over their friends' death is enough for them to try to kill each other.

The crew of the Archangel grieve for the apparent deaths of Kira and Tolle. Cagalli searches the wreckage for Kira but instead finds Athrun and confronts him for killing Kira.

The Archangel finally arrives in Alaska. A grief-stricken Miriallia attacks Dearka, now a prisoner on board the Archangel, but ends up saving his life when Flay tries to shoot him. Kira awakes and finds himself in the care of Lacus.

The crew of the Archangel find themselves questioned for their actions regarding their escape from Heliopolis, the fall of the 8th Fleet, and entrusting the Strike to Kira Yamato. Meanwhile, Lacus comforts Kira, who questions his right to live, especially after trying to kill Athrun.

Flay, Mu, and Natarle are to be transferred off the Archangel. Mu suspects that something is not quite right as the Alaskan JOSH-A base is evacuated. Flay is captured by Rau Le Creuset. Lacus and her father entrust Kira with the ZGMF-X10A Freedom, equipped with Neutron Jammer Canceller technology.

Operation Spitbreak is initiated, with both ZAFT and the Earth Alliance believing they have outsmarted the other. The Archangel is left behind to be destroyed in a calculated plan that would decimate everyone on the battlefield, until Kira arrives to save them.

Lacus, now denounced a traitor to the PLANTs for handing the Freedom over to an unknown pilot, confronts Athrun and challenges him to decide what he truly is fighting for. Athrun is ordered to pilot the ZGMF-X09A Justice to seek and destroy the Freedom.

Kira and the Archangel make their way to Orb, where Lord Uzumi welcomes them and asks that they decide for themselves why they are fighting. The Panama mass driver is destroyed by ZAFT in retaliation for the blow they took at Alaska. Meanwhile, Erica Simmons presents a reconstructed Strike for the Archangel crew's use.

To get a hold of Orb's mass driver, the Earth Alliance demands Orb to concede with them or be attacked for siding with ZAFT. Murrue decides the Archangel will support Orb and its crew members are discharged if they no longer wish to fight. Muruta Azrael, leader of Blue Cosmos, attacks Orb with three new mobile suits, the Forbidden, Raider, and Calamity. When Kira starts to have trouble with them, Athrun in the Justice arrives to help.

Athrun in the Justice assists Kira fight against the Forbidden, Raider, and Calamity. As the fight continues, the three Earth Alliance pilots argue with one another, but they are interrupted when they are struck by intense pain. The Earth Alliance are forced to retreat and regroup. The two friends reunite and Athrun must make a decision regarding whether he should continue obeying his father's orders or fight for what he believes in.

The Earth Alliance attacks again, but the results are the same as the previous battle. The Archangel and the Orb ship Kusanagi launch into space, while the leaders of Orb stay behind. They explode Orb's mass driver and armaments factories, sacrificing their own lives in the process.

Cagalli, though grief striken with her father's death, confronts Kira with a mysterious photograph given to her by Lord Uzumi, of a woman with two infants and Kira and Cagalli's names written on the back. On a PLANT, Lacus is still on the run for treason, but broadcasts messages to counter PLANT Supreme Council Chairman Patrick Zala's propaganda. She soon discovers that her father has been assassinated by Patrick Zala.

Athrun returns to the PLANTs on a shuttle to speak to his father, but he is arrested. Lacus and (the presumed killed in action) Andrew Waltfeld join forces, stealing the ZAFT support ship Eternal and rescuing Athrun. They join forces with the Archangel and the Kusanagi thus forming the Three Ships Alliance.

The newly-formed Three Ships Alliance take shelter at the abandoned Mendel colony. Unfortunately, they are tracked down by both ZAFT and Earth Alliance forces. Rau Le Creuset commands the ZAFT fleet and Captain Natarle Badgiruel, commands the Earth Alliance assault ship Dominion. Dominion takes the initiative and attacks with the mission of capturing either the Freedom or Justice.

The Dominion retreats so their pilots can get their medicine. Mu and Dearka enter the Mendel colony to confront Rau and Yzak. Kira comes to their aid and he and Mu are shocked to discover Rau has a few secrets to reveal.

Kira and Mu face terrifying revelations in an encounter with Rau. Dearka and Yzak have their own meeting where they question what they are truly fighting against. Meanwhile, the Dominion and the Earth Alliance once again attacks. Rau returns to his ship and sends Flay back to the Earth Forces.

Flay, who was held captive by Rau, is rescued by the Dominion despite Kira's desperate attempts to steal her lifepod. She gives Muruta Azrael the disk she was given by Rau which contains the specs on the Freedom and Justice and the Neutron Jammer Canceller technology.

Equipped with Neutron Jammer Cancellers, the Earth Alliance forces launch an all-out attack on the PLANTs. The Boaz military asteroid is destroyed by nuclear weapons with Earth Alliance's next target being the PLANTs. The Freedom and Justice arrive at the battlefield in time to destroy all the nuclear warheads. In retaliation, Patrick Zala orders to fire the GENESIS.

The GENESIS, a huge gamma-ray laser wipes out a large portion of Earth Alliance's forces. The Earth Alliance forces are forced to withdraw temporarily to regroup. During the intermission, each of the couples on board the Archangel, Kusanagi, and Eternal prays of each others safety in the upcoming battle.

GENESIS' second attack cripples the Earth Alliance's reinforcements and destroys their Ptolemaeus lunar base. The Three Ships Alliance save the PLANTs from the second wave of nukes. Mu fights Rau in the ZGMF-X13A Providence while Kira and Athrun fight the Forbidden, Raider, and Calamity. On the Dominion, Natarle becomes fed up with Muruta and orders the crew to escape. Muruta fires at the Archangel , but Mu sacrifices himself to protect them. In revenge, the Archangel fires and destroys the Dominion.

The Archangel, Eternal, and Kusanagi plunge into the battle, trying to keep both sides from using their weapons of mass destruction. Rau destroys Flay's escape shuttle, killing everyone on board. Flay's spirit visits the grief striken Kira to apoligizes and thanks him. Kira destroys the Providence with the Freedom, while Athrun remote-destructs the Justice to destroys GENESIS. With both the PLANTs and the Earth Alliance forces in disarray, the renegade moderate faction of the PLANTs seize the opportunity to call for a cease-fire, effectively ending the war.