C.E.70. The friction between the Naturals (the Earth Alliance) and the Coordinators (ZAFT), who seek to establish their own economic bloc, finally escalates into armed conflict with the "Bloody Valentine" tragedy. With its mobile suits, ZAFT is able to overwhelm the Earth forces on many fronts, but the war drags on longer than expected. Eleven months after the "Bloody Valentine," a young Coordinator named Kira Yamato is caught up in ZAFT's Gundam capture operation. Also involved in this operation is Kira's former friend Athrun Zala, who has become a ZAFT soldier. Amid the flames of war, the two are fatefully reunited. But in order to protect his Natural friends, Kira boards the Strike Gundam, the only one which has escaped capture, and now faces Athrun as an enemy...

In the year C.E.70, the conflict between the Z.A.F.T. Forces and the O.M.N.I. Enforcer has erupted into armed warfare of the highest intensity in the wake of the "Bloody Valentine" catastrophe. An armistice is signed following the Second Battle of Yakin Deyue, which saw massive casualties, but no armistice could extinguish the hostilities that existed between the Naturals and the Coordinators. Shinn Asuka finds himself caught up in the O.M.N.I. Enforcers' Orb Operation, and sees his parents and sister killed before his very eyes by the fighting.