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Set in 2131 AD, Deunan Knute, a young legendary female soldier is a survivor of the Third World War which has brought Earth to the brink of destruction.
Alongside her former lover and comrade Briareos, who is now a cyborg, Deunan is brought to a Utopian city called Olympus, also inhabited by a genetically-engineered species called Bioroids.
There, she integrates into the prestigious ESWAT organization to serve as the city's guardian. But what she discovers is not the promised land of peace, but rather a deadlier, more elusive battlefield than before.
Bioroids have a lifespan much shorter than those of humans, due to the suppression of their reproductive capabilities.
When the fluid that is used in Bioroid life extension processes is destroyed by the Olympus Regular Army in a terrorist attack as part of its demonstration of fear and hatred for the Bioroids, a crisis which requires immediate resolution is formed, and the Appleseed data is revealed to still exist, even though most thought it destroyed.
Under the surface, as we can see, Olympus is plagued by conflicting factions. Some believe that Bioroids are a threat to the future advancement of mankind, whilst others believe that humans themselves are the threat.
The ultimate question is over everyone's right to life, and whether or not one group deserves life more than the other. At the centre of this battle is Appleseed, the data that is able to extend Bioroid life, by restoring reproductive functions.
The daughter of Carl and Dr. Gilliam Knute, Deunan, who is considered as a beautiful and highly skilled warrior, has spent almost her entire life fighting in a war that was, for the most part, over.
It was not until she was rescued by an ES.W.A.T. (Extra Special Weapons And Tactics) team, led by Hitomi and her former lover Briareos, in the middle of a ruined city just after Deunan had a short but fierce battle with unidentified enemies, that she was finally evacuated from the Badlands.
When she arrived in Olympus, the change of environment was severe, but it was a greater shock to her when she found that Briareos had lost over 75% of his original body during the last Global War and was now a cyborg.
The day after she was brought to the city of Olympus, Deunan learned that over half of the population of the city was composed of artificial humans called Bioroids and that her new friend, Hitomi, was one herself.
Deunan also discovers that other people are looking for her, mostly because she possesses, without knowing it, the secret of "Appleseed". That interest will become extremely important when Hitomi's life will be at risk and the "Appleseed Data" will be needed to save her and the entire Bioroid population of Olympus.
But the discovery of the "Appleseed Data" could condemn the human population to extinction without Deunan knowing about this detail. But that would mean defying the powerful Olympus Regular Army (O.R.A.), composed entirely of humans and under the command of General Edward Uranus III and Colonel Hades.
At one time, Briareos was Deunan Knute's lover, as well as a comrade-in-arms in battle. During two years of hard separation for both of them, he was severely injured on the North African front. When Hitomi and the Elders saved him, he had over seventy-five percent of his body replaced by state-of-the-art mechanical components, making him a highly advanced cyborg.
During Deunan's stay in Olympus he is assigned by his ES.W.A.T. superiors to protect her and also begins to search for the "Appleseed Data." In the original story, Briareos was a black man from the Mediterranean who served under Colonel Carl Knute, Deunan's father.
In the original manga, Briareos and Deunan are not separated, and she is well aware of his cyborg body replacement.
Voiced by: Jūrōta Kosugi (Japanese), Jamieson Price also known as James Lyon (English)
Prime Minister of Olympus, Athena Areios is a first-generation Bioroid created by Deunan's mother, Dr. Gilliam Knute, and served as her lab assistant until Dr. Knute's death.
Because Athena is a first-generation Bioroid, she doesn't have the emotional limitations the second-generation has, so she has greater latitude to use "extraordinary" methods to try to find Deunan.
Of course, she also runs the risk that either the Council of Elders or General Uranus would find out and take action against her, so she, along with her chief-of staff Nike, have to be very careful.
Voiced by: Mami Koyama (Japanese), Mary Elizabeth McGlynn (English)
Nike is Athena Areios's chief-of-staff, as well as being commander-in-chief of ES.W.A.T. Although she is a second-generation Bioroid, and being such having her emotions controlled, she is fiercely loyal to Athena, not to mention the Bioroids' prime purpose: the salvation of humanity.
Voiced by: Miho Yamada (Japanese), Mimi Woods (English)
A second-generation Bioroid, Hitomi is charged with recruiting new members of ES.W.A.T.. She had led the rescue mission of Deunan Knute in the Badlands, as well as aiding her getting settled in Olympus. Although her emotions are regulated, she has interest in the emotion of love, and is disturbed by hate, as expressed by the human soldiers of the O.R.A, especially towards the Bioroids.
Voiced by: Yuki Matsuoka (Japanese), Sandy Fox (English)
Also a second-generation Bioroid, Yoshitsuni Miyamoto... or "Yoshi" as he is refered to, is ES.W.A.T.'s chief mechanic and Land Strider designer. He has a crush on Hitomi, but is unwilling to speak up about it. He also would like to further examine Briareos' cybernetic armor more closely, if Briareos would allow it. His knowledge of mechanical workings would become useful later in the film.
Voiced by: Toshiyuki Morikawa (Japanese), Dave Wittenberg (English)
 Edward Uranus III
Supreme commander of the O.R.A., General Edward Uranus III has a great distrust of the Bioroids, and wishes to either control them or totally eliminate them. But unlike his subordinate Hades, he is not given to irrationality. A friend of the Knute family, Uranus deeply regrets the death of Dr. Gilliam Knute and wants to persuade Deunan to help him in his quest.
Voiced by: Yuzuru Fujimoto (Japanese), Michael McConnohie (English)
Colonel Hades is Gen. Uranus's subordinate. Like Uranus, he has a great distrust of the Bioroids. However, his distrust has evolved into an irrational, all-consuming hatred, and wishes to see the Bioroids destroyed.
Originally, Hades served under Carl Knute, Deunan's father, in Los Angeles' S.W.A.T., but was thrown out by Carl because of his extreme methods. He held a grudge with Carl, and is furious that Carl's D.N.A. is in all the Bioroids.
Voiced by: Takehito Koyasu