Despite the name of the series, most of the characters are not samurai in the true sense of the word. In Japan, the name of the series is officially in katakana, but is alternately written in Kanji (侍魂, Samurai Damashii), with the second character pronounced supiritsu, "spirits", to better reflect the game's setting.
Twenty years pass, with the age of samurai and swordsmen drawing to a close. Those not abiding to the peaceful change of era are outlawed to a prisoner island. Zealous inhabitants rise up and try to create a "new world exclusively for the chosen ones", whom are intent on destroying the shogunate. The group they form is called the "League of the Three Blades of Domination" and the island becomes known as Ritenkyo. Their leader is an old man named Oboro. A member of the Shogunate, Seishiro Kuki, is ordered by his superiors to assassinate the ones responsible for the uprising. An older Haohmaru goes to find his "niece", Mikoto, and to free her from her torn past.