In Universal Century 0088, the Anti-Earth Union Group (AEUG) has emerged victorious in its war with the Earth Federation's Titans at the cost of devastating losses. Neo-Zeon, the third faction in the war formerly known as Axis Zeon, remains as powerful as ever. Led by Newtype Haman Karn, Neo-Zeon has been implementing plans to take over both Earth and the space colonies. The AEUG flagship Argama heads to the Side 1 colony Shangri-La for repairs. Living in the colony is Judau Ashta, a 14-year-old junk dealer who is struggling to make enough money to put his younger sister through school. Upon the discovery of an escape pod containing a former Titans pilot, Judau and his friends are quickly led to the Argama in hopes of stealing a mobile suit which they can sell for a fortune. However, with the arrival of a Neo-Zeon ship seeking to defeat the Argama, Judau and his friends are dragged into to a conflict that will bring them across space and Earth.

It is Universal Century 0087, and the One Year War between the Earth Federation and Principality of Zeon is over. The Earth Federation has created an elite task force, known as the Titans, who are responsible for hunting the remaining Zeon forces. However, the power-hungry Titans have shown themselves to be no better than Zeon, spurring the creation of a rebellious faction called the Anti-Earth Union Group (AEUG). 17-year-old Kamille Bidan lives in the colony Green Noa, home to a Titan base. Kamille gets in trouble after assaulting a Titan officer, an event that coincides with an attack led by former Zeon ace Char Aznable, now known as AEUG pilot Quattro Bajeena. When Kamille steals a Titan's prototype Gundam, he soon finds himself in the middle of the dangerous conflict.

After surviving a brutal terrorist attack on Plant Quetta, Suletta Mercury returns to dueling at the Asticassia School of Technology, while Miorine Rembran sits at her injured father's side, waiting to see if he will recover. As the residents of Earth House are preoccupied with their respective troubles, two members of Dawn of Fold—the perpetrators of the attack—secretly infiltrate the school, putting Suletta and her friends at risk. At the same time, Prospera, Suletta's mother, approaches Miorine to propose the continuation of Quiet Zero—a project headed by Miorine's father that can allegedly end all war. Prospera seems to be another political figure with hidden, opposing motives, and whether she truly has Suletta's well-being at heart remains to be seen.

In the year Cosmic Era 0071, the space colony Heliopolis remains neutral in the great war raging across the galaxy between Coordinators, human beings whose biological traits have been altered before birth, and Naturals, unaltered people who remain on the planet Earth. The Naturals' deep hatred of the Coordinators drove the advanced beings into space, seeking shelter in man-made colonies. Kira Yamato is a Coordinator and university student on Heliopolis, when his life is thrown into disarray as ZAFT, the military organization composed of rebellious Coordinators, attacks the colony in an effort to steal a set of five state-of-the-art military mobile suits known as Gundams. While ZAFT manages to make off with four of the mobile suits, Kira take control of the final Gundam, the Strike. Surviving the battle, Kira and his college friends join the crew of the Archangel, a ship run by the Earth Alliance, and the young soldiers experience the horrors of war and the loss that comes with it.