In year 74 of the Cosmic Era, the civil war raging between the earthbound Naturals and space-dwelling Coordinators comes to a close. Suffering a major setback, Kira Yamato pilots the Strike Freedom Gundam and leads the Archangel and its crew in a desperate bid to destroy the Requiem, a super-weapon intended to wipe out most human life in the universe.

Alongside Kira fights his best friend and rival Athrun Zala, an ace pilot who must defend himself against the wrath of his former subordinate Shinn Asuka, pilot of the powerful Destiny Gundam. Shinn believes Athrun to be a traitor, an obstacle in the course of the universe's peaceful future.

As life-or-death mobile suit brawls are waged for the fate of the galaxy, a sprawling war between humans who are incapable of understanding one another draws to its conclusion.