W środku XXI wieku pewna kobieta (Krysten Ritter) stara się rozwikłać zagadkę swojej tożsamości, gdy jej życie w przedziwny sposób splata się z życiem innych ludzi.

Æon Flux is set in a bizarre, dystopian future world. The title character is a tall, leather-clad secret agent from the nation of Monica, skilled in assassination and acrobatics. Her mission is to infiltrate the strongholds of the neighboring country of Bregna, which is led by her sometimes-nemesis and sometimes-lover Trevor Goodchild. Monica represents a dynamic anarchist society, while Bregna embodies a police state.

Set in Mexico City, the series follows the adventures of the eponymous wrestler in the role of a superhero who must try to stop the plans of Dr. Clone, an evil scientist. He is determined once again to kill him and creates clones based on his old enemies (thanks to their DNA), and use them to dominate the world.