Four centuries later, in 2415, the remaining five million humans inhabit Bregna, a dystopian[4] walled futuristic city-state, which is ruled by a congress of scientists. Although Bregna is largely an idyllic place in the destroyed Earth, people routinely disappear and the population has nightmares.
A skilled warrior, named Æon Flux, is a member of the Monicans, an underground rebel organization who communicate through telepathy-enabling technology and are led by the Handler. After a mission to destroy a surveillance station, Æon comes home to find her sister Una has been mistaken for a Monican and killed. When Æon is sent on a mission to kill the government’s leader, Trevor Goodchild, she discovers that both she and the Monicans are being manipulated by a cabal of council members working towards a coup d’état, unrelated to the goals of the Monicans.
Æon questions the origins of everyone in Bregna and in particular, her personal connection to Trevor. Everyone in Bregna is revealed to be a clone, grown from recycled DNA. With the dead constantly being reborn as new individuals and bearing partial memories of their previous lives, their troubling dreams have increased. Cloning was required because the antidote to the virus made humans infertile. Trevor’s ongoing experiments were attempts to reverse the infertility. His preceding clones had all worked on this problem. Æon learns that she is a clone of the original Trevor’s wife Katherine and that she is the first “Katherine” clone in over 400 years.