Flay, Mu, and Natarle are to be transferred off the Archangel and the Archangel is then ordered to go to JOSH-A. An Archangel crew member suspects that something is not quite right since Alaskan JOSH-A base is close to a ghost town. Flay is captured by Rau Le Creuset, but much to her surprise she is not treated as a prisoner. Operation Spitbreak is initiated, with both ZAFT and the Earth Alliance believing they have outsmarted the other. The Archangel is to be sacfriced in a calculated plan that would decimate everyone on the battlefield at the JOSH-A base.
Kenshin's resumes command of the team after making a full recovery from the previous battle consisting of Kira, Athrun and Yzak. his team withdraws just in a nick of time as the base self destructs. The sight of it further increases his hate for the Earth Alliance thinking out loud " now since they cannot win the war they decide to massacre everyone including destroying their own base...this is their idea of doing justice ?... "
Luckily the Archangel also escapes harm due to Kira warning everyone. Since the Archangel abandoned its post it has been declared a rouge ship, they then make their way back 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.
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.
The battle of Orb is also been seen by ZAFT forces. Kenshin then questions the Earth Alliance " are they really that dumb and stupid that they will fight themselves over stopping the war ? Is this war really gotten to a point where the battle is meaningless ? "
Kira seeing his former friends need help decides to launch despite orders telling him to stay he knows the consequences of his actions, he is then joined by Athrun in the Justice assists in the fight against Earth Alliance forces. 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.
Kira has made the decision to side with Orb in what he believes is the way to end the war now Athrun must decide 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-stricken 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 for leading a resistance broadcasting messages to counter PLANT Supreme Council Chairman Patrick Zala's propaganda. She soon discovers that her father has been assassinated by Patrick Zala.
Kenshin is now commanded to recapture or destroy the Freedom or Justice, just as the former CCO of the Archangel Natarle Badgiruel is given a new assignment.
Athrun makes the decision to return to PLANT to confront his father about the war but he is shot and arrested by Kenshin, on the orders of Patrick Zala the PLANT Supreme Council Chairman. Lacus and the presumed killed in action Andrew Waltfeld join forces, stealing the ZAFT support ship Eternal and rescuing Athrun. Before Athrun leaves he calls out to Kenshin to join him. Kenshin then decides to stick to his duty, his anger for the Earth Alliance drove him to stay loyal to ZAFT.
The Eternal then join forces with the Archangel and the Kusanagi thus forming the Three Ships Alliance.