The year is U.C.0105, twelve years after Char's Rebellion. "Mafty" has begun resisting the Federation government's tyrannical rule by assassinating its high-ranking officials. Its leader is actually Hathaway Noa, the son of Bright Noa, who fought in the One Year War alongside Amuro Ray.

A girl named Gigi Andalusia, who displays uncanny powers, has reminded Hathaway of a past trauma. Though he is bewildered by her words, he prepares to carry out an air raid on the Adelaide conference, determined to fulfill Mafty's goals and lay his own past to rest. While swayed by her cryptic words, he continues preparing for Mafty’s mission — the attack on the Adelaide Conference. Meanwhile, Kenneth Sleg of the Federation Forces prepares a defense operation for the Adelaide Conference and a plan to eliminate Mafty, when he is approached by Handley Yoxon of the Criminal Police Organization with a secret proposal. As Hathaway and Kenneth pursue their respective goals, Gigi also sets off for Hong Kong to fulfill her own role.

The year is U.C.0105, twelve years after the second Neo Zeon War (Char's Rebellion). The corruption of the Earth Federation government has accelerated Earth's pollution, and it has implemented an inhuman “Man Hunting“ policy in which civilians are forcibly exiled to outer space.

The anti-Earth Federation movement “Mafty” has begun resisting the Federation government through the extreme tactic of assassinating its high-ranking officials. Its leader Mafty Navue Erin is actually Hathaway Noa, the son of Federation Forces captain Bright Noa, a veteran of the One Year War.

Hathaway is striving to clear a path forward as a warrior, upholding the ideals and intentions of Amuro Ray and Char Aznable. His destiny, however, is drastically altered as he encounters Federation Forces Captain Kenneth Sleg and a mysterious young beauty named Gigi Andalucia.