Æon Flux was set in a bizarre, dystopian future world. The title character is a tall, leather-clad secret agent from the nation of Monica, skilled in assassination and acrobatics. Her mission is to infiltrate the strongholds of the neighboring country of Bregna, which is led by her sometimes-nemesis and sometimes-lover Trevor Goodchild. Monica represents a dynamic anarchist society, while Bregna embodies a police state—referred to on one occasion as a republic by Goodchild. The names of their respective characters reflect this: Flux as the self-directed agent from Monica and Goodchild as the technocratic leader of Bregna. Although Bregna is shown to be repressive, in the first full-length episode, “Utopia or Deuteranopia?”, Clavius, the president deposed by Goodchild, is described by a questioning journalist as having been democratically elected. In the same episode, an upper house of parliament is also mentioned by the character Gildemere.
Graphic violence and sexuality, including fetishism and domination, are frequently depicted in Æon Flux. In the featurette Investigation: The History of Æon Flux (included on the 2005 DVD release), Peter Chung says the visual style was also influenced by the animated series Rugrats; Chung had worked on Rugrats prior to Æon Flux and had been extremely frustrated by the limitations of the characters.
With the exceptions of the exclamation “No!” in the pilot and the single spoken word plop in the episode “Leisure”, all of the short episodes are completely devoid of intelligible speech. Instead, the sound track employs a variety of sound effects, including sounds such as laughter, grunts, and sighs. It would not be until the beginning of Season 3 that dialogue would be used much more extensively.
One peculiarity of the early shorts is the violent death of Æon Flux, which occurs in each installment. According to the commentary by Peter Chung in the 2005 DVD release, she dies in every short episode after the initial six-part pilot because he never intended to make more episodes and felt the best solution was to have her keep dying; by contrast, she only “dies” once in the half-hour series. Often her death is caused by fate, while other times she dies due to her own incompetence. One of the half-hour episodes, “A Last Time for Everything”, ends with the original Æon being killed and replaced by an identical clone. (In the episode “Chronophasia”, Æon is apparently killed repeatedly by a monstrous baby, but the reality of these events is ambiguous. In “Ether Drift Theory”, Æon is suspended indefinitely in an inanimate state, but remains technically alive.)
Although continuity is virtually non-existent in the original shorts — Chung made some adjustments for the 2005 DVD collection to improve this — the primary unchanging elements in the episodes are the two main characters of Trevor and Æon. For the DVD release, the main series was rearranged and grouped by director, making them more continual. A fourth season of half-hour episodes was considered, but never materialized. In late 2005, around the time the DVD collection was released, Chung announced plans to work on another Æon Flux project. In an online interview conducted after the release of the film, Chung indicated that it was to be a made-for-DVD animated feature. So far, nothing more has been heard of the project and it has likely been cancelled.