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 put into a lifepod and given a disk which contains the data of Neutron Jammer Canceller. Flay manages to get through to the Dominion and the Archangel, Kira also hears this and rushes to save her, but leaves himself unguarded, and the Freedom is shot in the head. Athrun saves the Freedom and takes it back to the Archangel. Meanwhile, the Dominion saves Flay. Back at the Archangel, Kira goes unconscious and when he awakes his friends and Lacus comforts him while he releases all his mental stress.

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 Masamune, 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.

While the Earth forces regroup Athrun talks to Kenshin " you seen what has happened come to your senses and fight with us , if this keeps going both Earth and PLANT will be destroyed. "

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. Kenshin finally decides to disobey the orders he was given and 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 telling the Archangel to destroy the Dominion in which it does so.

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. As Patrick Zala is gunned down by an officer after he decides to sacrifice even his own troops to attain victory, Kira destroys the Providence with the Freedom, while Athrun remote-destructs the Justice to destroy 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 ceasefire, effectively ending the war.