Having defeated Logos and the Earth Alliance, the triumphant Chairman Durandal now reveals his ultimate plan for humanity. The world reacts with confusion and horror to the details of the Destiny Plan, but Durandal has come too far to let anyone stand in the way of his dream of eternal peace and happiness. Using the weapons of his fallen enemies, the Chairman demonstrates that he will stop at nothing to create his new world. The Archangel and its allies are now humanity's last hope to prevent Durandal from carrying out his plans. Once again, a fierce battle begins around the Requiem cannon and its relay stations, and our lead pilots meet in a final confrontation over the lunar surface. Shinn against Athrun, Kira against Rey, Archangel against Minerva... In the end, there can be only one victor.

In C.E.75, the fighting still continues. There are independence movements, and aggression by Blue Cosmos... In order to calm the situation, a global peace monitoring agency called COMPASS is established, with Lacus as its first president. As members of COMPASS, Kira and his comrades intervene into various regional battles. Then a newly established nation called Foundation proposes a joint operation against a Blue Cosmos stronghold.

Following the success of the Dawn Rebellion, Degwin negotiates with Vice Admiral Revil to surrender all Federation assets and the complete withdrawal of Federation forces from Side 3 to prevent similar incidents from happening again. After bring reprimanded by Degwin for failure to look after Garma, Dozle sends Char - who motivated Garma into starting the rebellion - to Earth; in response, Char requests to become a mobile suit pilot when he returns. Feeling the burden of his responsibilities, Dozle proposes to cadet Zenna Mia. In the Earth city of Manaus, Char lands a job as a mobile worker pilot at a construction site. He meets a young Lalah Sune at a casino.

Cosmic Era 71. Mankind has developed into two subspecies: Naturals, who reside on Earth, and Coordinators, genetically enhanced humans capable of withstanding the rigors of space who inhabit orbital colonies known as PLANTs. The story revolves around a young Coordinator named Kira Yamato, who becomes involved in the war between the two races after a neutral space colony secretly developing mobile suits for the Earth Alliance is attacked by the PLANTs' military force, ZAFT.

Advanced Generation (A.G.) 101. The space colony Angel is attacked and destroyed by a mysterious "Unknown Enemy" with overwhelming strength. As this "UE" continues its attacks, a boy named Flit Asuno loses his mother when she is caught in the crossfire. Now in A.G. 115, Flit must fight using a new Gundam of his own creation, which evolves itself through battle. The curtain rises on an epic Gundam saga spanning 100 years and three generations.

When Banagher Links meets the mysterious Audrey Burne, he inherits the Unicorn Gundam and is swept up into the battle for space colony independence.

High-school student Amate Yuzuriha lives peacefully in a space colony floating in outer space. But when she meets a war refugee named Nyaan, Amate is drawn into the illegal mobile suit dueling sport known as Clan Battle.

It is the Universal Century, year 0153. The Zanscare Empire, which rules almost all of Side 2, has declared its independence from the old government, the hollow and corrupt Earth Federation. Under the justification of creating a new, space-based order, it has begun an invasion of Earth; and Point Kasarelia, the illegal residence area in Eastern Europe where Üso Ewin and Shahkti Kareen live, is no exception. As they are caught in the fighting between Zanscare and the opposing resistance organization, the League Militaire, fate draws Üso and his friends into the midst of battle.

U.C. 0097, one year after the opening of "Laplace's Box". Despite the revelation of the Universal Century Charter that acknowledges the existence and rights of Newtypes, the framework of the world has not been greatly altered. The conflict later dubbed the "Laplace Incident" is thought to have ended with the downfall of the Neo Zeon remnants known as the Sleeves. In its final battle, two full psycho-frame mobile suits displayed power beyond human understanding. The white unicorn and the black lion were sealed away to remove this danger from people's consciousness, and they should now be completely forgotten. However, the RX-0 Unicorn Gundam 03, which disappeared two years earlier, is now about to show itself in the Earth Sphere once more. A golden phoenix… named Phenex.

The Earth Forces has commissioned another Archangel-class ship, the Dominion; its sole mission is to destroy the renegade Archangel. As the battle draws to its ultimate conclusion, it is possible that humanity itself will be the victim. Kira, Athrun, and the others must stop a war that threatens both sides with genocide!