It is C.E. 71, and the Naturals of OMNI and the Coordinators of ZAFT continue to wage war. In their quest for power, ZAFT dispatches a team to seize Earth Alliance's latest mobile suits in the neutral colony of Heliopolis. Caught up in the midst of this turmoil is Kira Yamato, a civilian coordinator from Orb who is studying at a technical college on Heliopolis. Having witnessed ZAFT's acquisition of four out of five mobile suits, Kira stumbles upon the final one - the Strike - and is left with no choice but to commandeer it in order to save himself and his companion. As the chaos ensues, Kira unexpectedly encounters his childhood friend, Athrun Zala, now a ZAFT soldier and one of the hijackers. Despite possessing the Strike, Kira decides to join the Earth Alliance's Archangel vessel as a means of protecting his allies. Nevertheless, Kira grapples with feelings of disenchantment as he finds himself pitted against his former comrade and at odds with his own people.