Revolving around the love-hate relationship between Aeon Flux and Trevor Goodchild, Aeon remains unrelenting in completing her mission as a Monican assassin in attempts to bring down the fascist scientocracy, the Bregnan Government, controlling the last remnants of humanity. The game is set between the cartoon and movie timelines, as each chapter bridges the centuries of war between the Monicans and Breens, and it highlights the different eras of the politcal and personal conflict.