‘애플시드’를 사수하고 인류의 미래를 구하라! 서기 2131년. 우량종 복제인간 바이오로이드와 인간이 공존하는 최첨단 미래도시 ‘올림포스’. 평화로운 겉모습과는 달리 행정부를 장악한 바이오로이드로부터 권력을 되찾고자 하는 인간들의 반란은 본격화된다. 그리고 이를 지켜보던 원로들은 ‘애플시드’ 프로그램의 봉인을 해제하기로 결정하는데… 이제 인류의 미래를 위해 ‘애플시드’를 사수하기 위한 전설의 여전사 듀난의 전쟁이 시작된다!
The battle for the Capital city of Kyo rages as warring political factions vie for power against hereditary rulers. After the murder of her parents at the hands of her seditious uncle, a young girl named Kintoki flees to the mountains to lead a harsh life; she is renamed Kai Doh Maru by the local villagers. Rescued by Raiko, the Captain of 'The Four Knights' - honorable defenders who protect the peace of the city, she is raised within their group as a boy. Living among the Knights, she learns the practices of martial arts and develops into a skillful samurai, becoming a permanent member of their team. Now, as a young woman of seventeen, she begins to discover new feelings of passion and love for Raiko... but she also discovers that these new emotions cause a storm of jealousy and rage in another woman linked to her past.