It's the year 2415, and more than 400 years after a virus killed off nearly everyone on the planet, one vestige of civilization has managed to flourish in the self-contained and walled city of Bregna. Run by Trevor Goodchild (MARTON CSOKAS) and his advisory council that includes his younger brother Oren (JONNY LEE MILLER), the city-state seems idyllic, but unrest is underfoot.
And that comes in the form of an underground band of rebels deemed the Monicans by the government that desperately wants to quell any sort of uprising. That's led to people simply vanishing from the city never to be heard from again, prompting the rebellion's leader, The Handler (FRANCES MCDORMAND), to send her operatives into the highly protected, labyrinth-like headquarters to assassinate Trevor.
Her best assassin, Aeon Flux (CHARLIZE THERON), who manages to sneak in with Sithandra (SOPHIE OKONEDO), has a personal ax to grind with the leader since her sister, Una (AMELIA WARNER) was murdered by government agents despite having nothing to do with the rebellion. Yet, Aeon can't manage to complete the job as she experiences a range of emotions and fractured memories that cloud her judgment upon meeting the leader.
After she's captured, Trevor doesn't have her killed, thus raising the suspicions of Oren and the other council members who soon plot a coup against him. As Aeon tries to figure out what's going on, she must not only contend with Trevor and his powerful assistant Freya (CAROLINE CHIKEZIE), but also Oren and his crew as well as Sithandra who's been ordered along with others by The Handler to take out the operative who they believe has failed her mission.