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The episode starts with Æon catching a fly with her eyelashes. It then cuts to a battle between Monican agents and Breen forces, with Æon liberally mowing down dozens of soldiers, apparently on a mission to assassinate a Breen official, though most of them are already sick and dying from a strange disease carried by an azure beetle. 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. While going there, Æon sees Trevor and the woman fondling each other, and shows signs of longing for such treatment.

Æon and Trevor kiss through the windows of their transports, with the former being in a plane and the latter being in a train. As they do, Trevor uses his tongue to open up Æon's fake tooth and place a rolled up picture inside. After the two of them part, Æon spies an industrial vehicle driving past. Æon then retrieves the picture from her tooth to find it is a photo of a fellow passenger and a suitcase. She climbs out and moves along the side of the plane to spy on the man, who is reading documents from the same suitcase. Æon must jump mid-air to the back of the plane to get inside, but she misses and falls. 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.

On an assassination mission, Æon infiltrates her target's home via a maintenance ladder. On her entry she falls from the ladder, and notices she is spied on by a security camera. While walking down a hallway she notices a room where the security camera recorder is being kept, and enters. She goes to destroy the tape but at the last minute decides to review the footage. The picture is faulty because of a loose video jack shorting against an air vent. Æon goes to fix the connection but spills coffee on her gloved arm. Unnoticed by the departing Æon, footage of another intruder previously entering the building plays on the monitor. 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.

Æon enters her living quarters to find an empty container of eggs she was keeping in her refrigerator. She then finds that Trevor, who is in a cupboard displaying masochistic behavior, has eaten them all. 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. As the other agent walks away, Æon steps up to practice and flawlessly executes the complex routine. Later, she enters a spaceship and collects some of the same eggs seen earlier in her apartment. 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 embryo dies as a result of her probing.

Æon and her red-clad companion descend from the high floor of a sea base, carrying a key. As the two enter an elevator, they are attacked by Trevor, who is easily knocked out by Æon, but not before he pushes all of the elevator's buttons so that it will stop on every level. She handcuffs him, but drops the floor number attached to the key, forcing her to stop on every level. On each floor, Æon shoots up the stairwell to keep a pursuing Breen soldier at bay, tests the key on that floor's locker, and shoots a distant sky hook that is attempting to latch on to the railing of a small, distant platform just above water level. Each time she exits the elevator, Trevor and the other agent make out, then the agent springs back to either guard Trevor or try to retrieve the number as Æon re-enters.

The episode focuses on a massive battle between the Monican and Breen soldiers, all of whom resemble Æon and Trevor, respectively. During the course of the battle, Æon cuts down dozens of guards before she is knocked down by a Breen guard who had been playing dead. Æon sees another Monican agent creeping up on the guard and attempts to distract the latter, but the Breen sees the agent and kills both him and Æon. 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.

Trevor Goodchild has "temporarily" taken power in Bregna following the disappearance of the elected president, Clavius. 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. Gildemere, a Breen soldier loyal to Clavius, is plotting against the new Chairman, correctly suspecting that Trevor was responsible for Clavius' disappearance. Trevor's reasons for the coup are twofold: he gains ultimate power in Bregna, and uses Clavius' body to create an isolated place, locked with a strange ornate key, where he can keep Æon for good, keeping her to himself in perfect privacy. Æon allies with Gildemere and finds her way into Clavius, confronting Trevor and leading Gildemere to his leader, allowing him to free Clavius from Trevor's captivity. However, Clavius is revealed to be completely insane, and Gildemere is forced to kill him. He and Æon then fight, and she easily overpowers him.

Trevor is holding captive two humanoid birds called Seraph-Trevs, the female of which he is trying to seduce. Meanwhile, another scientist named Ilbren is obsessed with the female, even going so far as trying to employ Æon to capture it, offering her the male in return. Their meeting is interrupted by a mechanical tentacle, which Ilbren fends off with a swarm of robot wasps.

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. Unknown to Æon, Una is in love with the male Seraph-Trev, of whom she was previously sent a picture via messenger pigeon (the male seemingly sent out the bird with the picture as a call for help).

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. Una guides Æon through a network of tunnels, but when she realizes Æon's goal is the male Seraph-Trev's chamber, she sets out to find him herself while sending Æon on a roundabout route. Ilbren arrives and ties Trevor up, then makes his way to the female.

The episode starts with a pair of boys play-fighting, while another claps to mimic the sound of heavy punches. The latter boy later flicks a pebble into the path of one of the border turrets, activating it and watching the resulting spectacle. Trevor Goodchild is being pressured by the government into making the border more intimidating, despite his want to make people stay in Bregna through the "power of ideas." To this end, he secretly allows Æon to come in and bomb the factory where the parts for the wall are being made. Meanwhile, two Breen lovers, Onan and Sybil, seek to escape from Bregna into Monica through a gap in the frontier. The escape is almost a success, but one of the turrets shoots Sybil in the back, destroying one of her vertebrae. 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.

Trevor has perfected a method of copying humans. Determined to put an end to the operation, Æon and her fellow agent Scaphandra, a double-agent for Bregna whose feet have been replaced by hands, cross the border into Bregna. As Æon rushes towards Trevor's base of operations, Scaphandra is captured and taken to Trevor, who takes a sample of her for copying. Æon comes in, frees Scaphandra and interrogates Trevor about the ethics and inner purposes of his operation. Deliberately presenting an opportunity for Trevor, Æon allows him to take a sample of her, though she smashes Scaphandra's sample. After Æon leaves, Trevor copies Æon for himself.

This is revealed to be a complex plot by Æon to inflict maximum pain on Trevor by exchanging places with her copy, toying with Trevor's feelings, then allowing her copy to kill her. But as she performs her half of the mission, the original Æon begins to lose herself, developing feelings for Trevor and vice versa. But, while she is still herself, she orders her copy to kill Scaphandra. 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. The original Æon, who now looks and dresses very differently from her old self, comes and confronts the copy.

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. Trevor is determined to stop them, believing that the Demiurge will ensure a lasting peace for humanity. The rocket is successfully launched after a long and costly battle, but not before the Demiurge instils parts of itself in earthly avatars: a cat, a bird and a resurrected Monican agent named Zenith Nader (a play on zenith and nadir). 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.

Æon has gone to her apartment, an unstable structure supported by a single cable, and sees Nader's condition. Celia, apparently wanting to steal the bird avatar, infiltrates the home and is killed by Æon, without the assassin even seeing whom she has killed. Æon goes to kill Nader's "baby", but is too late to stop Trevor extracting it; it is a new humanoid form of the Demiurge. 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. Narghiles are a mysterious "controlled species", apparently immortal, that produce a memory-wiping drug called bliss. During her escape, Æon runs into a female prisoner called Muriel, whom she accidentally kills after Muriel mistakes her for a guard. After escaping with the photos, Æon encounters and leaves with a Monican named Rorty.

As they drive away from the prison, Rorty reveals himself to have been Muriel's partner, and Æon tells him of Muriel's death, but not of her role in it. Rorty tells Æon that, years before, he and Muriel had taken bliss, and lost their memories. 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 and Rorty begin to fall in love, and Æon agrees to participate in his plan to eliminate the narghiles. Æon takes the final narghile up to the platform, only to find that all the others are missing.

Trevor arrives and mistakes Æon for Muriel. 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 reveals her identity, and the two fight, which ends with Trevor escaping with the narghile. Meanwhile, Rorty discovers the compromising photos. Upon her return, the two argue; Æon reveals both that she killed Muriel and Muriel's betrayal.

The episode begins with Æon lying on a stone slab, waking from a dream in which she was screaming. It then flashes back to earlier, where Æon and Trevor are making their individual ways to a Breen research base researching an ancient virus that apparently causes insanity and formed a basic part of early humanity, until they developed an immunity. Æon is cornered by the Breen soldiers near the base, but is sucked down and finds that, although the base has been there for under a month, it looks like it has been derelict for centuries. There, Æon finds a young boy who guides her through the base and eventually shows her a vial of virus, the only intact vial out of a set of five. There is also a giant fanged baby, which appears to have been the first test subject for the virus, stalking the caves.

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. Lindze and Æon are there both to rescue Lindze's boyfriend, a scientist named Bargeld, and to destroy the facility. Soon after they arrive, Trevor and one of his human experiments arrive, destroying Æon's ship in the process, though the experiment is quickly subdued by a swarm of metal-sensitive wasps. 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 unwittingly spills a corrosive substance that begins to melt the base's walls, and everyone must escape before the paralyzing sea floods the base and traps them all. Bargeld tries to use his device for neutralizing the sea, but finds that the key to activate it is missing. Æon rushes back to find it.

Æon chases Bambara, a vicious criminal who frequently maims or kills those he encounters. Æon, ignoring his victims, pursues him through a train and onto a building site. Bambara escapes Æon, killing a construction worker in the process, but is captured for Trevor Goodchild. Trevor inserts a strange robot into Bambara through his navel, and Bambara suddenly loses his darker side, becoming friendly to those around him and quickly befriending an orphan. Trevor says the robot is a Custodian, an artificial conscience of his creation which he hopes to implant in all citizens. 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. Æon goes after Bambara's Custodian, successfully removing it, although she is drugged and captured by Breen forces.

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. Æon, determined to stop Trevor from using the satellite, steals and buries the remote. But, avoiding the search parties, she finds a hibernation pod holding a strange alien with removable eyes and psionic abilities, and lacking the ability to breathe or eat, or genitals. The alien is captured by one of the search parties, but saves Æon when its captor throws a fire bomb. Trevor examines the Alien and sees the signs of exposure to Aldis B.

He heads off to find the alien's ship, but the alien escapes and follows him, finding both him and Æon at the ship. Aldis B has killed off everyone on the ship, leaving only the alien, who had been awaiting rescue in its pod. Æon and Trevor make love in the ship, while the Alien watches. The next day, the alien finds Æon and offers her one of its own eyes, but Æon refuses. Then Æon offers to show the alien human sexual pleasure. The alien, either frightened or revolted by the idea, leaves and is captured by Breen soldiers. After getting better acquainted, the alien and Trevor travel in a special shuttle to the alien's amazing home world, while Æon decides to await Trevor's return in the hibernation pod.

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