A young boy named Jiro finds his mother and sister murdered in his home. Falsely accused of the crime, he flees from his village and meets a priest named Tenkai, who has him kill a rogue ninja named Tarouza. After fulfilling that task, Jiro undergoes training to become a master assassin. Many years later, Jiro finds out that he was an orphan and his real father was Tarouza, who had worked for Tenkai until he aborted his mission when he fell in love with an Ainu woman. The young ninja discovers that the Shogunate was to retrieve the lost treasure of Captain Kidd and use it to once again isolate Japan from the rest of the world. Using the clues that Tarouza had kept secret, Jiro - along with the female ninja Oyuki and a slave named Sam - travels to Russia and America to search for the treasure in hopes of using it to extract revenge from Tenkai.

In the future, Miko, a Japanese psychic warrior is looking to destroy a corporation that mass produces robots called "Shinobi" in order to avenge the death of her loved one.

Legendary samurai Jubei Yagyu must face off against a necromancer and his army of the undead in order to rescue Ohiro the young ninja girl from the clutches of Inshun Hozoin, the evil man slated to become lord of darkness on the eve of Armageddon. No living man is a match for Jubei's sword, but what skill can this mythic swordsman employ to defeat an army of the undead?