故事的舞台是在战争中被破坏的基地殖民地、飘荡着大量战舰的残骸的“Thunderbolt宙域”，宙域是对ZEON公国要塞“A Bao A Qu”的补给道路，为了夺回宙域，地球连邦军和ZEON公国展开了激烈的战斗。地球连邦军的伊奥·弗莱明少尉等人乘坐GM204F，潜入Thunderbolt宙域，向狙击手发起了挑战。

After the Dawn Rebellion, Char travels to Earth and meets a girl with mysterious powers named Lalah Sune. Meanwhile, Amuro's father Tem Ray is working on the RX-78 development project. Learning of the defection of Doctor Minovsky, a key figure in Zeon mobile suit development, he heads for the moon. History's first battle between mobile suits unfolds in the twilight zone of the lunar surface. Then comes Universal Century 0079. Side 3, the space city furthest from the Earth, launches a war of independence against the Earth Federation government under the name of the Principality of Zeon. An era of violent upheaval begins, in which half of the total human population will be killed...

In the year UC 0071, three years after escaping the Zabi faction on an Ocean Cargo ship, Artesia and Casval are living happily in Andalusia, Spain, Earth under the identities of Sayla Mass and Éduoard Mass, respectively; masquerading as the children of Don Teabolo Mass, a long time friend of their father Zeon Zum Deikun.

Universal Century 0068, Side 3 - The Autonomous Republic of Munzo. Zeon Zum Deikun attempts to declare complete independence of Munzo from the Earth Federation Government, while he preaches the evolutionary potential of humans who have advanced into outer space. Deikun however suddenly falls to his death in the middle of his speech at parliament. Upon Deikun's death, Jimba Ral spreads word of a House of Zabi conspiracy - but despite such efforts the power and sphere of influence of House of Zabi, led by Degwin Sodo Zabi, only seem to escalate. While we witness for the first time the untold convulsions of Universal Century history, Casval and Artesia, just bereaved of their father, must face destinies which will be just as tumultuous as the very era itself.

U.C. 0096, three years after the end of the Second Neo Zeon War. The mysterious Vist Foundation attempts to hand over a certain secret to the Neo Zeon remnants known as the Sleeves. This will mean the opening of Laplace's Box, which holds a great secret tied to the origins of the Universal Century. The exchange is to take place at the manufacturing colony Industrial 7, home of the student Banagher Links. When Banagher rescues a girl who gives her name as Audrey Burne, he is drawn into the conflict surrounding Laplace's Box.