During the One Year War of U.C. 0079, the Earth Federation and Principality of Zeon engage in a fierce battle at the "Thunderbolt Sector", a shoal zone in the former Colony Side 4 "Moore". After successfully infiltrating Zeon's sniper field, ace Federation pilot and jazz enthusiast Io Fleming is given control of the latest Gundam prototype.

The second movie of the long-awaited fan favorite Thunderbolt Series. Earth, eight months after the end of the One Year War. Captain Monica launches a secret mission, "Operation Thunderbolt," and selects Io to pilot the Atlas Gundam. She leads the assault landing ship Spartan into a part of the ocean effectively controlled by the South Seas Alliance. Their objective is to secure or destroy the data of the Psycho Zaku, which the Alliance now possesses. Daryl, who took the upper hand in his battle with Io, has descended to Earth as part of the remnant forces of the Principality of Zeon. He has also been given the mission of obtaining information on the Psycho Zaku. Fighting alongside his new comrades, Io encounters Commander Peer, the South Seas Alliance's border garrison commander. In the sea, on the ice field, and among the thick jungle, the mobile suits of Zeon, the Federation, and the South Seas Alliance battle each other. "The war is not over yet."

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.

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.

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.

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.

A voice draws two destined individuals together for a showdown, awakening 1/12-scale statues of the Nu Gundam and Sazabi, leading to a fierce battle inside the mall.