Even with all the casualties, the fighting continues. Flay’s shuttle, by abandoning the Dominion, wanders into the area where Freedom Gundam and Providence Gundam are violently fighting. Flay is still not able to get over Kira and the shuttle strays off as if drawn to him. But then, right before Kira’s eyes, Flay is killed by Rau’s ruthless attack. Kira cries out in agony, thinking he once again failed to protect who he should protect. He then suddenly finds himself in a void with Flay’s spirit and has a vision of her. Did her soul finally touch Kira’s soul with her life coming to an end…?
In the meantime, Patrick sets the next target of GENESIS on Earth. However, seeing the craziness in some of his actions, even a ZAFT commander come to have doubts and disagrees with Patrick, and tries to stop him. Athrun breaks into Jachin Due with Cagalli to stop his father’s madness. As they barge in, they see Patrick shot down by an officer who tried to stop the massacre of GENESIS. Even in his last moment, Patrick murmurs cursed words towards Naturals and dies from his wounds.
But even his death could not stop the rampage. GENESIS is set to fire when Jachin Due start to self-destruct. Athrun heads inside GENESIS alone. He plans to self-detonate the Justice Gundam inside GENESIS to cause a nuclear explosion. Athrun prepares to self-destruct along with Gundam but Cagalli stops him, and they escape together.
Around the same time, the final duel between Kira and Rau ends with them striking down each other at the same time. Eileen Canaver and other former Clyne Faction loyalists in PLANT call for an cease-fire and a path to peace seems to have finally opened. Athrun is overcome by despair at the horrific ruins of battle before him. Just then, Birdy flies out into space. Further ahead, the wreckage of Freedom Gundam lies, and next to it floats, Kira… There is still hope.