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In UC 0087, seven years after the end of the One Year War and following the events of Operation Stardust, the Earth Federation establishes the elite counter-insurgency division called the Titans to hunt down remaining pockets of Zeon resistance. The Titans become overzealous in their mission, resorting to brutal methods to achieive their goals, becoming nothing more than ruthless tyrants with an ambition to rule the Earth Sphere. Two anti-Titans resistance groups, the AEUG (Anti-Earth Union Group) and their Earth-bound counterparts Karaba, form to unite various existing forces in the struggle against the fascist-like Titans. Their members consist of renegade soldiers of the Earth Federal forces, former soldiers of the Principality of Zeon and militia from space colonies. Most notable is Bright Noa, who returns as captain of the assault cruiser Argama, the flagship of AEUG space fleet, and Quattro Bajeena, the pseudonym of legendary ace pilot Char Aznable.

Kamille Bidan is a troubled civilian youngster from Side 7's Green Noa 1 colony. His personal resentment towards the Titans results in him joining the AEUG. Quattro takes Kamille under his wings and becomes his mentor. The series also sees the partnership and cooperation between Kamille and One Year War hero Amuro Ray, and the tension between Amuro and Char. Behind the frontlines, the AEUG and Karaba are supported by many companies on Earth and in space. Besides financial support, manufacturing giant Anaheim Electronics provides logistics and technical support for the AEUG, including spaceships, mobile suits and munitions.

The series begins when Quattro raids a Titans military base in Green Noa 1 to acquire intelligence on a new mobile suit prototype dubbed the "Black Gundam". Kamille is caught up in the raid and helps the AEUG steal the Gundam. Eventually, he joins the AEUG, initially as the Gundam's pilot, until he receives the Ζeta Gundam (made by Anaheim Electronics and based on Kamille's own design). Things are complicated further as Paptimus Scirocco, a "contract killer"/mobile suit developer from the Jupiter Energy Fleet (who, unbeknownst to his government handlers, is an extremely powerful Newtype) executes his own plan. He secretly conducts a coup d'état and usurps the Titans' leadership as part of his ambition to dominate the Earth Sphere. The war between the Titans and the AEUG soon escalates as Haman Karn, the true leader of Axis Zeon, joins the war, leading to a three-way conflict.