In the year 2011, a devastating virus wiped out 99% of the world's population. The remaining survivors live in the idyllic city of Bregna, but like all post-apocalyptic utopias, everything is not as it seems. Æon Flux is a member of a rebel group known as the Monicans who seek to undermine the government (or something), but when her sister Una is taken on suspicion of also being a Monican (she's not) and Æon is sent to kill the government's leader, Trevor Goodchild, she ends up uncovering secrets about Bregna that pretty much throw her ideas about herself and her world down the stairs.
This film contains examples of:
- Adaptational Modesty: Æon's costume is much more modest than it was in the cartoon, both because of general decency standards and simply because the cartoon costume probably would never stay in position, even if adhesives were used.
- Adaptation Dye-Job: Trevor is blond in the cartoon, while he has black hair in the movie. His brother Orin is the blond one.
- Ancient Keeper: The genebank zeppelin, the DNA archive floating above the city, is guarded by the Keeper, an incredibly old man who explains the plot at the end.
- Big Bad: Vice Chairman Orin Goodchild is given the role and acts as a much more traditional villain than Trevor did in the original work, scheming to keep the remnants of humanity under his iron-fisted control.
- Cain and Abel: Trevor is actually mostly good in this continuity, and his brother Orin is doing all the bad stuff and plotting to depose him.
- Canon Foreigner: Trevor's brother Orin, who didn't exist in the cartoon.
- City in a Bottle: In the film, Æon is a Matrix-style opposition guerrilla out to bring down her closed city which is straight out of Logan's Run, her lover is a totalitarian Reluctant Mad Scientist trying to keep secret the human race's sterility while he solves it, and the actual villain of the piece is the RMS' brother, an entirely new character who believes that their current existence is perfect and that a cure would be just as bad as revolution.
- Cool Airship: The huge zeppelin circling the city, which proves to be a gene bank.
- Decomposite Character: The Anti-Hero/Anti-Villain Trevor Goodchild becomes two characters: the heroic Trevor and his blond villain brother Orin.
- Elite Mooks: The common Bregnan soldiers wears black uniforms with red markings that leaves their eyes exposed, but at one point Aeon and Trevor are hunted by a squad of Special Operatives clad in grey, wearing face-plates and wields heavy, automatic weaponry and knows how to use them, putting up quite a fight and even managing to inflict near-mortal wounds on Trevor. Even Aeon has difficulties trying to take down these mooks.
- Enemy Mine: Trevor and Æon are forced to team up when the depth of Orin's nastiness becomes obvious.
- Expy: Orin basically has some of Trevor's evil traits from the cartoon.
- Eye Scream: Æon must authenticate herself by being dosed with an anesthetic before a needle is inserted in her eye to test her DNA.
- Faceless Goons: The Bregnan soldiers are all masked.
- Garden of Evil: The defenses of the "government zone" are biotechnologically engineered plants with poison and ballistic weaponry.
- Gatling Good: Freya's weapon is a multi-barreled rotating handgun.
- Genetic Memory: Somehow, due to being clones people can recall memories of their genetic predecessors. This causes mental illness in the population as flashes of them bleed through. It also serves as kind of biological Past-Life Memories with Aeon. In the Goodchilds' case though they simply passed them down.
- Handy Feet: Sithandra, who had a second set of hands grafted onto her ankles—a procedure which she highly recommends to Æon.
- Heel–Face Turn: Trevor ends up turning heroic when he discovers all of the evil his brother has been getting up to.
- Last Bastion: Bregna is claimed to be the last inhabited human city.
- Lighter and Softer: The original animated series had much more graphic violence and some disturbing sexual content. The film is tamed enough in both aspects to be rated PG-13.
- Mythology Gag:
- At the start of the film, Æon grabs a fly with her eyelashes, as in the intro of the cartoon.
- Trevor died an unknown number of times. Because they were clones. (Although actually Trevor only dies twice at most in the cartoon series, in "Tide" and possibly in one timeline of "Chronophasia," it's Æon who keeps dying. The movie has Æon die only once.)
- Neck Snap: Aeon kills more than one enemy by snapping their necks with her legs, including a mook trying to sneak upon her in the prologue.
- Nothing Left to Do but Die: The Keeper gives up and dies of old age after Æon and Trevor enter the airship and learn its secrets.
- La Résistance: The Monicans. who are struggling to bring down the Goodchild regime.
- Reincarnation Romance: Æon turns out to be a clone of the wife of the original Trevor, and they fall in love inevitably as a result.
- Scope Snipe: One of the Monicans backing up Aeon in the final shootout was killed when a mook shoots her through the scope, with a first-person shot of the lens breaking.
- Sound-Only Death: Claudius is taken away and shot off-screen, with the gunshot audible.
- Spy Catsuit: Not as stripperiffic as in the animated series (in equal parts to keep the censors happy and to obey the laws of physics), but the Monicans do love their spandex.
- The Starscream: Orin acts as the Vice Chairman to his older brother but quickly puts into fruition his plan to seize Trevor's position for himself.
- Town with a Dark Secret: The plague that struck in 2011 sterilized the survivors. The Goodchilds have been keeping humanity going through secret cloning while Trevor and his clone descendants look for a cure, but the memories of the clones' past lives were starting to bleed through, slowly driving the population mad. Secret within the secret: not only did he find a cure, but women were starting to conceive naturally. But Orin had the test subjects and the pregnant women murdered to keep this a secret and keep them in control. He even went so far as to attempt a coup in order to keep his secret.
- What Happened to the Mouse?: Or What Happened to the Elite Mooks. The Special Forces sent after Aeon and Trevor lose most of their men in the subsequent shootout, but at least two were still around shooting as Aeon and Trevor escapes into a train. Somehow they don't show up for the rest of the film, and in the climax the opposing forces consist entirely of regular Bregnan troops.
- What Measure Is a Mook?: Despite pontificating about the value of the individual, Æon and Trevor slaughter huge numbers of Faceless Goons with no problem whatsoever. It's particularly glaring given the deconstruction of this trope in several episodes of the cartoon series.
