The city of Edo, the 18th century. Owaka, the daughter of a merchant family, and her childhood friend Matsukichi. The two were drawn to each other, but Matsukichi has been disowned by his family, and is working for the city fire brigade. Meanwhile, negotiations begin for the arrangement of Owaka's marriage. Unable to let go of her thoughts of Matsukichi, her mad emotions make her bring about a massive inferno which razes Edo. By chance encounter, the two meet again amidst the fires.It is an epic spectacle set against the stage of the massive metropolis of Edo.

In the Kanto region of Japan, seven high schools take place in a turf war for territorial supremacy: Nanyo Academy, Kyosho Academy, Seito Academy, Yoshu Academy, Rakuyo High School, Gogun High School, and Yoshu Private School. The fighters of each school bear the sacred jewels called magatama, which contains the essence of warriors from the Three Kingdoms era of Ancient China 1800 years ago, as well as their fates.

Immediately following the events of "Ikki tousen: Xtreme Xecutor", the kids from Nanyo Academy head to Kyoto for a school trip. Before long, they run into rival classmates from other Kanto schools and find themselves confronted by Kyoto's best fighters. It's a battle of epic proportions. Hopefully the city of Kyoto will be left standing!

Masane Amaha and her daughter Rihoko are on the run from a government child welfare agency that wants to take Rihoko away from her mother. They are caught and Rihoko is taken away. Meanwhile, Masane is attacked by an advanced weapon that can disguise itself as a human being. When faced with the danger, a strange light emits from her wrist and she transforms into a powerful being. She becomes involved in a power struggle between powerful organizations, with her at the center of their attention because she holds the greatest power of them all, the legendary Witchblade.

The Diclonius, a mutated homo sapien that is said to be selected by God and will eventually become the destruction of mankind, possesses two horns in their heads, and has a "sixth sense" which gives it telekinetic abilities. Due to this dangerous power, they have been captured and isolated in laboratories by the government. Lucy, a young and psychotic Diclonius, manages to break free of her confines and brutally murder most of the guards in the laboratory, only to get shot in the head as she makes her escape. She survives and manages to drift along to a beach, where two teenagers named Kouta and Yuka discovers her. Having lost her memories, she was named after the only thing that she can now say, "Nyuu," and the two allow her to stay at Kouta's home. However, it appears that the evil "Lucy" is not dead just yet...