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.