Japan in the Nineteenth century is torn by warfare and rebellion. Small bands of soldiers try to overthrow the Tokugawa Shogunate. Kenshin, a young orphan boy whose is taken in and who's fighting skills were developed by great swordsman Hiko. But Kenshin, his hopes for a new world peace at odds with his life full of blood and killing.

The story starts out with Kenshin as a young boy named Shinta. He's being brought to a village to be sold into slavery along with other people, but they encounter a group of bandits. They are slaughtered although the women's last plea are for Shinta's life. Just as it seems that fate is to cut short Shinta's life, Hiko shows up and saves him.

Hiko is a mysterious lone swordsman in the story, but after easilly killing the bandits, he takes Shinta under his wing to teach him his unique sword fighting style.

Once Hiko decides that Kenshin's training should end, Kenshin joins up with Katsura to bring about a new world order and become a master assassin for him.