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 ministers. Its leader is actually Hathaway Noa, the son of Bright Noa, who fought in the One Year War alongside Amuro Ray. Haunted by past trauma, Hathaway is drawn to a mysterious girl named Gigi Andalucia, whose strange powers stir memories within him. While swayed by her cryptic words, he continues preparing for MAFTY's mission — the attack on the Adelaide Conference. Kenneth Sleg of the Earth Federation Forces prepares a defense operation for the Adelaide Conference and a plan to eliminate MAFTY and 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.