전작으로부터 6년후의 세계. 서드라 불리던 인간에 가까운 안드로이드 아미테이지는 로스와의 사이에 요코라는 딸을 두고, 이름까지 바꾼채 화성에서 살고 있었다. 그러던 어느날 반물질 플랜트에서 안드로이드의 반란이 일어나 이를 무력으로 진압하던 스트링스가 인간지상주의자로서 영웅으로 부각된다. 그러나 이 사건의 이면에 숨겨진 음모를 밝히기 위해 아미테이지는 홀로 지구를 향하는데...
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.
