As the fighting continues, Lacus asks ZAFT to not fire GENESIS because they are only repeating the mistakes from before. Rau flies through space and is surprised when he finds the wreckage of the Strike Gundam. Murrue cries because Mu promised her he'd come back. Kira pulls away from Athrun and tells him to look after Cagalli. Fires break out all over the Archangel, and Murrue sits in her chair and cries over Mu. Rau sees that Azrael was of no help to him, and he prepares to attack the Archangel. Dearka attacks him, but Rau deploys his funnels and overwhelms Dearka. Kira arrives and fires all of the Freedom Gundam's and METEOR's weapons, but Rau senses his presence and dodges the attack. His funnels then attack the Buster Gundam and severely damage it. Kira attacks with the METEOR's beam saber, and Rau tells him he shouldn't be alive because if people knew he existed they would want to be Coordinators like him. Rau uses his funnels against Kira, which forces Kira to eject damaged parts of the METEOR. As they fight, an insane Clotho attacks Yzak and Dearka. Yzak defends Dearka and uses the Buster Gundam's rifles to destroy the Raider Gundam and kill Clotho. Kira continues to attack Rau with the METEOR, but Rau dodges his attacks and uses the funnels to cause further damage to the METEOR. Kira tells Rau that he is what he is and there is more to him than just his strength. Kira sees Flay's shuttle and ejects from the METEOR just as it explodes. He flies towards her shuttle, and Rau directly targets the shuttle and fires. Kira blocks the shot with his shield and looks at Flay. One of Rau's funnels fires from above and destroys the shuttle. Kira cries out and suddenly finds himself in a void with Flay's spirit. She tells him that she is sorry and says she never understood anything because she was always in pain and afraid. She tells him she is free now and asks him not to cry anymore. Kira then goes into SEED mode and chases after Rau. The Kusanagi and Eternal fire all their weapons at GENESIS, but they have no effect due to GENESIS' powerful Phase Shift armor. Inside Jachin Due, Patrick sets the next target of GENESIS for Washington, D.C. on Earth.
Athrun ejects his METEOR and asks Cagalli to help him destroy Jachin Due's control center because they have no time left. Kisaka sends several M1 Astrays out to help cover them. Rau then begins to attack the Eternal and Kusanagi. Kira fires at him, but Rau senses the attack and dodges. Athrun and Cagalli head for Jachin Due and break into the fortress. Kira and Rau continue to fight, and Rau says the destruction of humanity is something that is destined to happen. Yzak and Dearka return to the Archangel, and Murrue wonders how everyone else is doing. Kira tells Rau that he's perverting the truth and that humans aren't as he says they are. Rau continues attacking and blows off the Freedom Gundam's shield and right leg. Captain Yuki disagrees with Patrick and tells them they've already won the war and there's no need to fire at Earth. Patrick shoots him with a gun and prepares to fire GENESIS despite the fact that ZAFT forces are in the line of fire. Yuki then pulls out his gun and shoots Patrick several times. Athrun and Cagalli then barge in, and all the officers run away. Patrick asks Athrun to fire GENESIS and dies from his wounds. Athrun runs over to a computer console and sees that GENESIS is set to fire when Jachin Due explodes. ZAFT forces begin to retreat from Jachin Due, and the Archangel joins up with the Eternal and Kusanagi under Yzak's protection. Athrun and Cagalli then return to their Gundams and head for GENESIS. Kira continues to fight Rau, and Rau says that it's pointless for Kira to fight because he'll lose when GENESIS fires. Cagalli asks Athrun what he plans to do, and he says he will self-detonate the Justice Gundam inside GENESIS to cause a nuclear explosion. He tells her to turn back and ejects his backpack to block her path. Rau blows off the Freedom Gundam's right arm, and Kira pulls out his double beam saber with his left arm. Athrun prepares to self-destruct, and Cagalli tells him what he's doing is escaping. Rau blows off the Freedom Gundam's head as Kira charges, but Kira sticks his beam saber through the Providence Gundam's torso. Jachin Due self destructs, and GENESIS begins to fire. Kira gets out of the path of GENESIS, and the Providence Gundam is destroyed. The Justice Gundam explodes, and GENESIS ceases firing and explodes. A cease fire is announced between ZAFT and the Alliance. Cagalli and Athrun come out of the Strike Rouge's cockpit and see Torii fly by. Kira floats in space next to the ruined Freedom Gundam and wonders why he's come so far. He looks up and sees Torii flying towards him, followed by the Strike Rouge.