In the Cosmic Era a war rages between the Earth Alliance and Zaft Forces. After 11 months of bloody war, the ZAFT forces secretly capture 4 of 5 prototype mobile weapons (Gundams). During this battle, Kira Yamato, a member of the EAF, encounters his best friend, Athrun Zala, now a member of ZAFT. Now on opposite sides of the war, Kira and Athrun must struggle with their thoughts as they are repeatedly forced to fight each other.