In the world of the Cosmic Era, the conflict between genetically enhanced Coordinators and unmodified Naturals has erupted into full-scale war. The Natural-dominated Earth Alliance, struggling to catch up with the Coordinators' superior technology, has secretly developed five Gundam mobile suits at a neutral space colony. Through a twist of fate, a young Coordinator named Kira Yamato becomes the pilot of the Alliance's prototype Strike Gundam, and finds himself forced to fight his own people in order to protect his friends.