The animated series:
- Alternate Aesop Interpretation: The "War" short is clearly meant to deconstruct The Protagonist trope, but it can also be seen to say how War Is Hell. We see both sides of the eponymous war from the point of view of the various "protagonists," and all of them are shown to have sympathetic motives.
- Alternative Character Interpretation: Some fans have theorized that the main characters might actually suffer from schizophrenia, hence their behaviour about wanting to achieve their missions and kill each other one moment, and fraternizing and bedding each other the next.
- The talkie shorts have several very different portrayals on the morality and competence of its two main characters. The Aeon on "Isthmus Crypticus" and "Thanatophobia" is moral up to a point, for while she very much indeed partays in her anarchistic terrorism she goes to lenght to help others she perceives as being manipulated or trapped. Meanwhile the Aeon on "Utopia or Deutoronopia?" is intensely amoral and has no real objectives besides screwing with Trevor. Trevor, too, can go from a justifiable Tyrant ("Utopia or Deuteranotopia?") to an egotystical idiot obsessed with control ("Isthmus Crypticus"). Whether or not either is driven by sincere belief on order or chaos and see their counterparts as mere playthings or whether everything they do is part of their BDSM-ish game is, as well, changing constantly between episodes.
- Designated Hero: Æon is the main character of the series, but some of her actions will make you question her morality, most poignant would be her acts of terrorism, using her allies (without telling them) to achieve her goals, getting them upset when they find out they've been had, and not being apologetic about it. The only indicator that Æon's a "hero" at all is that Trevor, her rival, is set up as an Evil Overlord from the get-go.
- Les Yay: Between Æon and Una. No longer the case at the end of the episode.
- Spiritual Adaptation: The talkie episodes strongly resemble an Animated Adaptation of The Cornelius Chronicles, with Æon and Trevor as Gender Flipped versions of Jerry Cornelius and Miss Brunner.
- They Wasted a Perfectly Good Character: In "Ether Drift Theory", a new character with a very interesting design is introduced as Trevor's bodyguard and a possible Worthy Opponent to Æon Flux. No sooner than two seconds later, she is taken out by a swarm of bees, and never seen or referred to again. What the?! Though knowing this series, it's probably intentional.
- True Art Is Incomprehensible: Peter Chung believes so.
"For me, a degree of ambiguity, or mystery, is the key ingredient of any artistic statement."
- Uncanny Valley: It may be the art style, but Æon's character design looks less sexy and more dangerously anorexic these days. You will also see things like a character with fingers where her toes should be, another with a spine that is capable of twisting around gates and a Gross-Up Close-Up of people eating cabbages.
- What an Idiot:
- There are quite a few moments in the show, but two that stand out are: Æon attempting to do acrobatics on a plane in flight (which causes her to fall to her death, something which she lampshades by giving herself a Face Palm), and Sybil attempting to escape Bregna through a passage that Trevor was already aware of (and even says so a few scenes before), which results in her losing both of her legs when the latter places traps there.
- Trevor can come across as this as well, often leaving gaping holes in his security that Æon and others have taken advantage of over and over again, that could easily get him killed if Æon was more competent. With that said: Who makes air vents in a prison that are big enough for a person to walk through, with poor lighting along the patrol corridors that allows for easy concealment in the shadows?
- Somebody whose conflict with the "hero" is basically just an elaborate BDSM roleplay.
- The Woobie: Sybil from "Thanatophobia".
The live-action film:
- Complete Monster: Vice Chairman Oren Goodchild is the traitorous younger brother of Chairman Trevor Goodchild and the Big Bad. Oren and Trevor rule a society that was rendered sterile by a vaccine Trevor used to save humanity from a virus 400 years in the past, cloning people and faking pregnancies to hide the sterility from the public. While Trevor intends to find a cure for the infertility, Oren wants to remain an immortal dictator, even as each new generation of clones suffer from increasingly worse nightmares. Ruthless about keeping power, Oren feeds information to a resistance group in the hopes they will assassinate his brother, staging a coup to become Chairman when the attempt fails; and kills every woman who becomes naturally pregnant.
- Inferred Holocaust: At the end of the film, people who have lived 400 years within Bregna decide to leave the city for the untamed jungle. And even with fertility reoccurring, there is no guarantee that everyone of child-bearing age is fertile. (In fact, it was only about 20 women in the whole city who had become pregnant in Goodchild's sample group.)