The film takes place 400 years into a post-apocalyptic future, after a virus has wiped out ninety-nine percent of the Earth's 2011 population. The survivors inhabit Bregna, a walled city-state, which is ruled by a congress of scientists. Æon Flux is an assassin-member of the 'Monicans', an underground rebel organization led by The Handler. When Æon is sent on a mission to kill the government's leader, Trevor Goodchild (Marton Csokas), she uncovers that she is the unwitting part of a secret coup. This discovery brings into question the origin and destiny of everyone in Bregna; and in particular, Æon's personal connection to the man she has been sent to assassinate.

The film incorporates numerous elements from episodes of the TV series, most notably the episode "A Last Time For Everything," as well as from Æon Flux: the Herodotus File, a graphic novel that was based upon the series.

• Official movie website