Æon Flux está ambientado en un extraño y distópico mundo futuro de criaturas mutantes, clones y robots. El personaje principal es una agente secreta de Mónica, alta, vestida con un traje insinuador, hábil en asesinatos y acrobacias. Su misión es infiltrarse en las fortalezas del vecino país de Bregna, liderado por su némesis a veces amante, Trevor Goodchild. Mónica aparentemente representa una sociedad anarquista dinámica, mientras que Bregna encarna un estado centralizado y científicamente planeado. Los nombres de sus respectivos personajes reflejan esto: Flux como la agente autodirigida de Monica y Goodchild como el líder tecnocrático de Bregna.

Liquid Television is an Emmy Award–winning 1990s animation showcase that appeared on MTV. It has served as the launching point for several high-profile original cartoons, including Beavis and Butt-head and Æon Flux. The bulk of Liquid Television's material was created by independent animators and artists specially for the show, and some previously produced segments were compiled from festivals such as Spike and Mike's Sick and Twisted Festival of Animation. Mark Mothersbaugh composed the show's theme music.

There were also a large number of animation pieces adapted from the work of Art Spiegelman's comic compilation, RAW. RAW featured underground cartoonists such as Mark Beyer, Richard Sala, and Peter Bagge. In particular, Dog-Boy by Charles Burns was based on the artist's series from RAW.