Eighteen months after the Bloody Valentine incident, the war between the Earth Alliance and the PLANT colonies had been twisted into an escalating campaign of genocide against each other by madmen who had seized control of their respective sides. The Earth Alliance OMNI Forces, under the influence of Blue Cosmos, had begun shifting its focus to the extermination of all Coordinators, subjugating any of the remaining neutral nations that would not join them. In the PLANTs, Patrick Zala, now Supreme Council Chairman, had shifted ZAFT’s war effort towards wiping out all Naturals in the name of vengeance and genetic supremacy, becoming increasingly unhinged as he executed anyone who spoke out for treason.
And as both sides raced closer and closer towards mutually assured destruction, a third force began to emerge to stop the escalating conflict between Naturals and Coordinators before it could destroy the world. This ragtag force was comprised of rogue Alliance personnel based on the warship Archangel, ZAFT dissidents based on the warship Eternal, and surviving Orb troops based on the warship Kusanagi, all united in desperation against the corrupting influence of Blue Cosmos and the tyrannical Zala.
History would come to know them as the Three Ships Alliance.