Seijiro Hiko, the thirteenth master of the Hiten Mitsurugi school, is wandering down a country road. He stumbles upon a caravan under attack by bandits, but by the time he gets there, everyone's dead except for a young boy. Hiko kills the rest of the bandits, and after some deliberation, he takes the boy, whose name is Shinta, under his wing. When he starts training Shinta in the Hiten Mitsurugi school, however, he decides that his name is far too gentle for a swordsman and tells him to start calling himself Himura Kenshin (meaning heart of sword) from now on.

As the years go by, Japan progresses into the Bakumatsu, and Kenshin thinks that they should join in the war. Hiko, however, disagrees, because he says that the Hiten Mitsurugi Ryu is far too powerful to be used for war. Kenshin persists, and Master and student part on bad terms. After little trouble, Kenshin finds himself an assassin for the Ishin Shishi faction.

Hundreds of men fall by his hand and his lightning-fast Battou-jutsu, and he earns the name Hitokiri Battousai. (Hitokiri means killer-- or shadow, if you want to romanticize it) One day, however, on a routine assassination, he gets a slash on his cheek by the young man he was supposed to kill. The young man was not very skilled, but even when he was wounded and bleeding, his determination to see his fiancée kept him going. Kenshin kills him easily after their exchange of blows, coming away only with a single wound to his cheek. Anyway, a few weeks after, he meets a woman named Tomoe and ends up taking her home with him. When the battle takes a turn for the worse (the Shinsengumi are winning), the Leader of the Ishin tells him to take Tomoe and hide out with her, posing as husband and wife. They do so, but Kenshin tells Tomoe that he cannot simply 'pretend' to be her husband. If they are to be living with each other, he'd rather they get married for real.

So they get married and live peacefully in their house for a few years, until Tomoe's old faction gets in touch with her. They find out that she's been living with the great Hitokiri Battousai, and want her to tell them his weaknesses. She's in love with Kenshin, by then, so she lies and tells them he is easily killed when asleep.

They are not impressed, and tell her to return the following day with better news. She does, but they take her hostage and say that she is Battousai's weakness. Kenshin goes after her, of course, and starts killing everything in sight. When he reaches the leader, however, he gets ready for the killing stroke, and Tomoe jumps in between them. She'd realized that he was slowly reverting to the hated Hitokiri he'd been suppressing their married life, and when she jumped between the two, she thought he would be able to stop. His killing stroke, however, was too powerful to reverse, and he ended up running her through. She gives him a slash running opposite his first, and dies in his arms.