As hundreds of soldiers die in the sewers, Trevor Goodchild finds and takes in one of the beetles, hiding it in a compartment under his fingernail and carrying it with his lover to the top of the building where Æon's target is sleeping.
Realizing she will die from the fall, Æon considers shooting herself, but is distracted by the industrial vehicle from earlier stopping at the edge of a cliff.
While washing her arm, Æon accidentally sprays water on herself in the bathroom's shower, forcing her to take the time to comb her wet hair.
Angry, Æon leaves her apartment, but before venturing outside the Monican base, she witnesses another female agent fail to successfully complete jumping through a complex climbing frame.
Resisting the urge to leave, Æon breaks one of the eggs, analyzes the broken contents under a portable microscope, and finds an aggressive embryonic form of a strange alien.
The Breen makes his way into the battle, slaughtering dozens more attackers, before he encounters a long-haired, super-fit Monican agent (called Romeo Svengali in the DVD commentary) with a sword.
In its third and final season, Æon Flux became a standalone program with each episode given a half-hour time slot with commercials.
Soon, Trevor enacts a policy of supposed "complete openness", actually a pretext for a surveillance state, as he installs cameras all across Bregna, giving him ultimate control over the people.
The male Seraph-Trev is securely held in an isolated chamber, reduced to a state of abject misery due to separation from his mate.
Æon plans to free them from Trevor's – and Ilbren's – designs, and to do so employs an old friend of hers named Una to translate directions to the Seraph-Trevs' chambers.
Una falls asleep and dreams of the Seraph-Trev rather than translating the directions as Æon asked, but the two infiltrate the base the next day anyway.
Now she can only stand up straight when a special ampoule is inserted, though when she takes it out she has otherwise impossible flexibility, making crossing successfully a stronger possibility.
But as she performs her half of the mission, the original Æon begins to lose herself, developing feelings for Trevor and vice versa.
The copy carries out Æon's request, pretending to cross the border with Scaphandra and hanging back, allowing the turrets to cut down her treacherous partner.
Æon and the Monicans have captured an astral being called the Demiurge, which is threatening to dangerously warp people's view of the world, and are preparing to launch it into space.
Over the course of the episode, the three avatars meet different fates: the bird is captured by Æon in a Monican morgue and apparently vanishes; the cat is nearly killed by Nader's lover, Celia, who was obeying her lover's last request to her, but prevents its death only to fade when alone; and Nader is taken to a Breen base for experimentation, where he begins to show signs of pregnancy.
As the Demiurge's power manifests itself in people nearby as extreme positive and negative emotions, Æon and Trevor fight over it as it rapidly grows to maturity, taking on a physical form similar to its host.
Celia is resurrected by the Demiurge and carried to safety – taking refuge in Æon's home – when suddenly the supporting cable snaps and the building collapses.
Disguised as a guard, Æon infiltrates a Breen prison where Trevor is keeping compromising photographs of them having sex, with the price of their return being a narghile.
Not remembering who they were or what lives they had had, Rorty and Muriel set out to capture every narghile alive and launch them all into the sun on a special platform they maintained high above their home.
Æon realizes that Muriel had betrayed Rorty, carrying on an affair with Trevor while handing the narghiles over to him, thus giving him exclusive control over bliss.
Æon and her fellow agent and friend Lindze infiltrate a secret Breen base called the Habitat, a place where mutants and artificial lifeforms live in a stable environment, surrounded by a sea of liquid which induces paralysis in any life-form exposed to it.
Bargeld is terminally ill from an artificial disease and has developed a way of changing the composition of the paralyzing fluid around the base, allowing all the people trapped there to swim to safety.
Æon then meets up with an organization of women who are opposed to Trevor's project, planning to remove the implanted Custodians and bring the operation to an end.
Trevor has designed a satellite called Aldis B, which will help speed up the evolution of humanity, but could also kill off half the living population of the Earth.