Ghost Dog lever på taket av en forlatt bygning sammen med en flokk duer. Her lever han etter ordene i den gamle samuraiteksten "Hagakure". Etter at en mafiagangster reddet livet til Ghost Dog ble han hans beskytter og tar oppdrag som leiemorder for ham. Men når han blir sveket av mafiafamilien reagerer han helt etter boken: Etter "The Way of the Samurai".

Even though Gennosuke and Oboro are from rival ninja villages, they are secretly in love. At an annual conference with the Lord, it is dictated that a competition--a fight to the death--will take place between the five best shinobi from each village. Gennosuke and Oboro's love is made even more impossible when they each got picked as the leader of the five to represent their respective villages.

An innocuous comment during a weapon inspection wounds the pride of low-ranking samurai Shinpachi, leading to an argument with his superior. The situation snowballs out of control, leading to a deadly duel and political fallout which threatens the entire clan. Declared mentally unstable by the corrupt authority, Shinpachi begins his descent into true insanity…

A noble samurai serving the Shogun as 'Kogi Kaishaku-nin' (Official Executioner) is the target of a plot by the evil Yagyu Clan to take away his position and replace him with a member of their own family. When his wife is murdered and evidence is produced that he was plotting against the Shogun the Code of Bushido calls for him and his son to commit sepuku. Instead he defies the Shogun's orders and takes up arms against his enemies, becoming an assassin for hire.