In the year 123 of the Universal Century, skirmishes between the Federation government and the rebel group Crossbones Vanguard echo across Earth's space colonies. One of these small battles breaks in the hometown of young Seabook Arno, forcing him and his friends to flee and ensnaring them in the political turmoil that is quickly evolving into an all-out war. Seabook meets Cecily Fairchild, granddaughter of the aristocrat Meitzer Ronah, who seeks to create a new political power called "Cosmo Babylonia." Using the Crossbone Vanguard as its muscle, the Ronah family schemes to restore aristocratic rule and establish an economic system that will benefit the nobility, thus devastating the quality of life for the common people of the Earth Sphere. Seabook is tasked with piloting the Gundam F91, a mobile suit created by his mother, and must choose between protecting the status Federation's status quo or cooperating with Cecily to find a better way of life for all.

In the year Regild Century 1014, an entire millennium has passed since the end of the fabled Universal Century, where legends like Amuro Ray and Char Aznable ruled the battlefield as ace mobile suit pilots. The Earth's surface that was once hotly contested is now mostly abandoned, with humanity preferring to live in space colonies and the surface of the moon. Capital Guard Academy student Bellri Zenam lives a peaceful academic life, but his normal days are brought to an end with the capture of pirate pilot Aida Surugan and her mobile suit G-Self. Bellri feels a strong mental connection with the G-Self and discovers that he is able to pilot it. He soon finds himself in contention with the "Capital Guard," a radical faction that follows its own secret agenda despite the wishes of the Amerian Army, who still hold power on Earth. Joining the crew of the Amerian spaceship Megafauna, Bellri and Aida must pilot the G-Self to victory against the Capital Guard and its leaders, the charismatic Colonel Kunpa Rushita and the enigmatic Captain Mask.

When the Golden Race invited other races to join them in the stars, three sentient races answered their call. The Goldens called them the Bronze, Silver and Heroic Tribes. Just before the Gold Tribe left to travel to another Universe, a fourth race appeared, traveling to the stars on their own accomplishments. The Golds named the human race the Iron Tribe. During the passing of time, humanity suffers at the hands of the more dominant races and is now facing extinction. Following a prophecy left by the Gold Tribe, Princess Deianeira sets out to search for the powerful being who might be able to save humankind. She meets a wild haired boy on an abandoned planet—a fateful encounter that will not only change the fortunes of Humanity, but also the fate of the universe.

The story revolves around Nikolai, apparently a part-cyborg; Galory, a young boy who apparently is part human/part Crest person, and Althea, who is entirely a Crest person. Seems the Earth and the Crest people were at war for 300 years so there's still a lot of bad feelings present. The ship Galory, Nikolai and others are on is ambushed and almost everyone killed by some kind of automated attack ships from a huge Crest ship that has been taken over by an automaton. Galory, Nikolai and Althea go to the ship to try and see if there are any survivors of an advanced party from Galory's ship that can be saved, and to see if they can destroy the Type 38 automaton in the ship's core.