In 2131 AD Deunan Knute has been a soldier on countless battlefields for most of her life. When the World War ends, she is transported to the city of Olympus to live peacefully and finds out that, in an effort to protect the human race from future wars, humans have created the Bioroids, a genetically enhanced race of people that have restrained feelings and therefore cannot hurt each other.

She also discovers, however, that not everyone is happy with this Human-Bioroid symbiosis: many humans treat Bioroids as a lower species and as a threat to their future. The human-controlled military is seeking to annihilate all Bioroids, and the Bioroid-controlled government is afraid of a coup d'état.

The task falls on Deunan to control the situation, and to avert the inter-species war. In this she is aided by her former lover, Briareos, who has lost his body in war, to become a cyborg — a brain in an artificial body.

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Alternative version: Appleseed
Sequel: Appleseed Saga Ex Machina
Other: Appleseed XIII
Alternative setting: Appleseed Alpha