Aeon Flux is a 3rd person action game inspired by the 2005 movie of the same name. The story takes place 400 years in the future after the majority of Earth's population has been wiped out by industrial disease. Only one city, Bregna, remains. The city is run by the group of scientists who had discovered the vaccine to prevent the disease, but a group of rebels known as the Monicans oppose their rule.

You control the main character of the story, Aeon Flux. Aeon is a skilled fighter, and can perform light and heavy strikes, combo attacks, and a variety of acrobatic attacks. When an enemy has only a small amount of health left, you also have the ability to perform a takedown attack; when successful this will award you a bonus, such as extra health. Aeon has a health meter and a style meter; when the health meter is depleted, the game is over. The style meter is filled by attacking or killing enemies; when you have earned enough style, you can charge up your combo attacks for extra damage. Aeon is also equipped with a gun called the FUG (Flux Universal Gun) as well as various gadgets. To use the gun you will need ammo which can be picked up at various locations on each level. The various gadgets and gizmos available need to be used to get past certain areas and solve some puzzles; intel capsules provide you with important data, small orbs can be controlled to disable alarms and activate doors, Aeon can hide in rollers to navigate through areas undetected, and more.