Æon Flux is set in a bizarre, dystopian, future world of mutant creatures, clones, and robots. The title character is a tall, bondage gear-clad secret agent from Monica, skilled in assassination and acrobatics. Her mission is to infiltrate the strongholds of the neighboring country of Bregna, which is led by her sometimes-nemesis and sometimes-lover Trevor Goodchild. Monica apparently represents a dynamic anarchist society, while Bregna embodies a centralized, scientifically 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.
Aeon on a flying plane, Trevor on a train are French kissing in the window. We find out he had put something in her false tooth, and they seperate as this transaction is done. While all alone, she looks at the picture, which includes a guy and a brief case. She heads outside of the plane and spies on the guy who she is looking for. She tries for the back door, but misses, and starts to fall to her death. Aeon decides to kill herself, but notices something different on ground. The enemies are pulling something put from the canyon, but she doesn't know what it is. She uses her binoculars, to get a better look, while falling. She then uses her gun as a grappling hook as she falls near the train tracks. She brings her eyes back to the binoculars, unaware that the rope she used is wrapping around her neck and free falling at the same time.
Aeon breaks into a place, where she is fasinated with a video. Before she can do anything, she is shot. As she dies, she looks at the video to see who shot her... it was Trevor.
Æon enters her living quarters to find some one had disturbed a container of eggs she was keeping in her fridge. In a kitchen cupboard, she finds a deformed Trevor (or a clone of Trevor) chained up, licking an egg. Æon leaves her apartment, but before venturing outside the Monican base, she witnesses another agent fall and fail to successfully complete jumping through a row of training grids. Æon steps up to practice jumping through, just as the other female agent walks away, and flawlessly executes the acrobatic and complex jumps through the training grids. Later, she enters an alien spaceship and collects some of the same eggs seen earlier in her apartment. She's agonising while trying to resist breaking one of the eggs. Her desire to play with the embryo is stronger than her good sense to get out of the ship quickly before the parent alien comes. She analyses the broken contents under a portable microscope and finds it to be an aggressive infant form of an alien. On her way out Æon is confronted by an adult, four-legged, and extremely tall alien, but holds up one of the eggs and threatens to break it if the alien attacks her. She runs away, and the alien triggers a grid barrier similar to the one at the Monican training base. Æon jumps through it with ease, but its revealed that the alien can use its four legs to navigate the barrier much faster. It swiftly catches up to Æon and kills her from behind. This episode contains the only English dialogue heard in the first season: the single word, "Plop." Given the title of the episode and the image of the mutated Trevor's ecstatic consumption of an egg in the beginning, it's hinted that the alien eggs may be a recreational drug, and the mission to retrieve more eggs could be optional. But may also be financially motivated if the drug were meant to be sold.
Aeon and her friend must stop a device from entering this device that would cause the place they are on to sink. Aeon and her friend is also hunting for an item behind one of the locked doors on one of the floors. Unfortunately she doesn't know which one since, Trevor through the key and tag in back of the room, and had pressed all of the elevator buttons (they are on the 7th floor, so from floors 6 to 1) She handcuff him to a bar in the room, and gives her friend a gun incase he does anything. She grabs the key and tries to grab the tag, but it's too late, the doors for the elevator is opening. She tries the key on the door (6th floor) but it doesn't open. While heading back to the elevator, she shoots the device, preventing it to enter the other device. She then heads back to the elevator, and tries to get the tag, but fails, when the doors open again. She tries the key but it won't open. This happens several more times, and Aeon then gets suspious over her friend, when she
Aeon tries to go to the enemies main base and ends up killing everyone, or so she thought. As she looks around, unaware that someone is still alive, he holds a gun to her head. He is about to kill her, but she sees someone (someone on her side) that might be able to help her. Aeon tries to stall the killer by flashing her tongue, but the enemy isn't stupid. He kills Aeon, and the person behind him. The enemy (who just killed Aeon) look over a wall only to see 50 (or more) of Aeon's people and starts to kill them all. He rushes onto their base, and starts to kill a lot of them (as with Aeon did with their people.) He starts to enter their main base and sees a door open. He is then be caught in a fight with a Samurai guy. After some fancy moves, the Samurai makes a direct hit with the enemy. A little girl emerges from the room, and the Samurai looking guy pats her on the head, before locking her in when more alarms go off. A plane full of their enemies start to take over the pla