After an opening introduction to a bloody scene of a futuristic World War 3, one soldier named Deunan becomes tranquilized. She then awakens several weeks later inside an operating room, frightened and on guard. From here, we learn that while unconcious, she has been brought to a place described as a Utopia called Olympus. It is here that she learns of a society that is trying to prevent the existence of warfare. By doing so, they feel it necessary to have half the population be human, while the other half be half-human, half-machine - otherwise known as Bioroids. These Bioroids are not allowed to reproduce, but instead, are allowed to receive "life extension procedures."Deunan also learns that her lover, Briareos, has undergone a serious injury during the war and in order to survive has become a cyborg. Because Bioroids are half-machine, their ability to feel emotion has been diminished significantly, but not completely. Thus, Briareos tends to seem rather cold toward Deunan due to his surgery. Due to Bioroids having a diminished capacity to feel emotion, it is believed that anger will no longer be a large part of this Utopia - thus ending war.
However, behind closed doors, the human military is taking every step carefully because frankly, they do not trust the Bioroids. The Bioroids too are taking every step carefully, mainly as a means of defense. Ironically this means that there is a silent war going on that the regular citizens of Olympus are not aware of.
Deunan befriends Hitomi, a Bioroid who looks exactly like a human. The city of Olympus is run by several forces - mainly Athena (a bioroid) and a council of elders who obey the will of Gaia, the inhuman force that governs Olympus.
As the human army becomes more distrustful of the Bioroids, they decide to bomb the main center in which the Bioroids get their life extension procedures done in order to ensure that Bioroids have no future beyond those that currently exist.
Athena, being a Bioroid herself, becomes fearful of the future of her kind, and in a meeting, it is revealed by the 7 human elders, that the Bioroids' only hope lies with Appleseed, a piece of data that only a select few even know exist. Appleseed, if downloaded and used correctly will actually ensure that Bioroids will be able to gain the human ability of reproduction. Seeing as how life extension is no longer an option, this is the Bioroids' only chance at survival.
On the way to retrieve the Appleseed data, Deunan and her team reach the main control room and activate a hologram that will reveal the location of Appleseed. In the hologram, we see Dr. Gilliam (Deunan's mother) hard at work in the control room. We hear young Deunan (probably about 7 years old) come in the room. It is here that we discover that her father was the first Bioroid, and her mother was one of the originators of the Bioroid technology. Also in the hologram, we see Deunan and her mother having a loving discussion, and her mother entrusts a pendant that she called Appleseed to her. Obviously this means that the data is in the pendant. She tells young Deunan to only entrust Appleseed to Athena, and nobody else. The hologram ends with the human military coming in and killing her mother for starting the Bioroid life cycle.
Deunan, after watching the hologram realizes she has had the pendant her whole life and brings it out of a hiding place (her gun). It is here she realizes that now is the time she should entrust Appleseed to Athena. But on the way out, the human military ambush them and try to force them to not give Appleseed to Athena because Bioroids cannot be trusted. Briareos, being a Bioroid himself, defends himself but the military won't hear of it. It comes down to brute force, and Deunan and Briareos jump off the rail into the water to avoid being shot, but Briareos get shot several times, while Deunan gets a perfect headshot at General Hades's head on the way down.
Now, they must find a way to save Briareos, and still get Appleseed into Athena's hands before total chaos rips Olympus apart.