Æon Flux is set in a surreal, futuristic universe of mutant creatures, clones, and robots. The title character is a tall, sexy, scantily-clad secret agent from the society 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 sworn enemy, and sometimes lover, Trevor Goodchild. Monica represents a dynamic anarchist society while Bregna embodies a centralized scientific planned state. The names of their respective characters reflect this: Flux as the self-directed agent from Monica and Goodchild as the technocratic leader of Bregna.

The term Æon comes from the Gnostic notion of Æons as emanations of the God, who come in male/female pairs (here Flux and Goodchild). This juxtaposition also maps accordingly to the characterizations of Eris and Greyface in the Discordian mythos. Further mythic parallels can be drawn in likening Goodchild to Apollo and Flux to Artemis.

Many of these motifs are shared with the science-fiction novel The World of Null-A.

The visual style of Æon Flux was deeply influenced by the figurative paintings and drawings of the Austrian artist Egon Schiele. Other key influences on Æon Flux can be found in Japanese anime (especially grittier fare like Akira), and European comic works such as the work of Moebius (particularly in lineforms, color palettes, and figure characterizations); Æon Flux is often erroneously classified as an anime series. Graphic violence and sexuality, including fetishism and domination, are frequently depicted. In the featurette Investigation: The History of Æon Flux (included on the 2005 DVD release), Peter Chung says the visual style also was influenced by the children's animated series, Rugrats, which he worked on prior to Æon Flux and found highly frustrating in the limitations of what the characters could do.

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) dialogue and consist primarily of sound effects and non-morphemic utterences (laughter, grunts, sighs, etc). (Unintelligble dialogue, particularly in season one, was voiced by the series music composer.)

One peculiarity of the early shorts is the violent death of Æon Flux, which occurs in each of the installments (by contrast, she only "dies" once in the half-hour series). Often her death is caused by fate; sometimes 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. Although continuity is not non-existent in the series -- and Chung made some adjustments for the DVD release to improve this -- the only unchanging continuity between half-hour episodes is the two main characters of Trevor and Æon. There is intentionally no continuity between the shorts. Peter Chung has said that this plot ambiguity and disregard for continuity are meant as a satire of mainstream action films, and his stories often emphasize the futility of violence and the ambiguity of personal morality.