When the series was continued three years later, it underwent several significant changes. The characters were finally given dialogue, and episodes were expanded to a half-hour format in order to fill their own time slot. The audience was finally given clues as to the motives of the central characters (namely Aeon Flux and her nemesis/love Trevor Goodchild), although much was still left unexplained. The writers worked hard to keep the feel of the series consistent with the shorts from the previous two seasons, and episodes maintained their mysterious appeal. The biggest change was that Aeon stopped dying in every episode.

The story was set at some unspecified time in the future. Two rival nations, Bregna and Monica, bordered one another and had polar opposite forms of government. Monica was a free nation with no official rulers or head of state (how it functioned remains unclear), while Bregna was an oppressive state with little regard for human rights.

Aeon Flux was a Monican agent who worked to topple the insidious designs of Trevor Goodchild, head of the regime that ruled Bregna. Mr. Goodchild, however, deigned himself a visionary for the human race and believed the people under his rule would best be served by his intervention and the denial of personal freedom (he was continuously hatching some maniacal scheme to reshape humanity). The stories were filled with moral ambiguity, and raised more questions than they attempted to answer.