In the world of the Cosmic Era, war rages between the genetically enhanced humans known as Coordinator and those who remain unmodified, the Naturals, who dominate the Earth Alliance. Struggling to catch up with the Coordinator's superior technology, the Alliance secretly develops its own Gundam mobile suits. But through a twist of fate, a young Coordinator, Kira Yamato, becomes the pilot of the Alliance's prototype ... and is forced to fight his own people in order to protect his friends.