The episode features a clone of Æeon. They quickly hatch a plan, which makes sense only in Æeon Flux's universe: The original will seduce Trevor, then be killed by the clone, with the unique goal of causing Trevor psychological suffering. The plan goes awry when original AElig;eon Becomes The Mask and falls in love with Trevor for real, regrets the plan, learns to see the good in Trevor, and ends up killed by her clone, who didn't approve of the development.
But, maybe AElig;eon knew she'd fall in love with Trevor from day one - the plan, then, was even more cruel than it seemed - Æeon didn't want Trevor to think she loved him, then witness her death; she wanted to really love him. So, she was giving up not only her life, but also her happiness, to make Trevor suffer.
Due to their constant infighting and a vicious cycle of destruction and reconstitution, humanity has reached a point where it is losing touch with its crucial aspects. Best exemplified in “A Last Time for Everything”, where the sanctity of human birth and uniqueness is rendered trivial by Trevor Goodchild’s cloning program. Trevor himself notes how humans are little more than a collection of amino acids. In “The Demiurge”, a faction of humanity is literally trying to be rid of an actual divine being, so their authority cannot be challenged (The Monicans). Another connection to the divine is “Isthmus Crypticus”, where humans seek angel-like creatures, either in order to covet their beauty, like Trevor, Ilbren and Una. While Æon’s actions in this episode seem altruistic, it’s actually a reflection of her atheism (possibly installed in her by the Monican government). “End Sinister” is about purging the human condition completely, in an attempt to become something more. Æon notes to Trevor when he embraces the influence of an apparent extraterrestrial.
“Ether Drift Theory” is about reducing the sanctity of life as a concept, by perverting it with unnatural, artificial creations that Trevor creates in The Habitat. “Chronophasia” is about the insane futility of human aspirations, a reflection of the Monican’s constant conflict with the Breens (for no apparent reason). It is also about the burden of guilt as Æon sees the faces of all the people she’s manipulated over the course of the series, thus far, when staring at the malformed fanged baby. Lastly, episodes like “Thanatophobia” and “Reraizure” is about humanity’s habit of betraying ourselves and those we love for our own selfish wants (i.e. Onan and Sybil’s desires for freedom or Rorty’s yearning for peace of mind).
