When a raid of murderous bandits ambushes a caravan of travelers in 1850's Japan, a passing swordsman possessing the most powerful of all sword techniques -- Hiten Mitsurugi-ryū -- swiftly dispatches the threat, but sadly not in time to spare the caretakers of a young red-haired boy named Shinta who is the sole survivor of the massacre. Taking pity on the boy, the swordsman, Soujiro Hiko the 13th, takes Shinta under his wing as an apprentice. He renames him "Kenshin", a name he considers to be more appropriate for a swordsman.

Following several years of training, Kenshin leaves his master to take part in the revolution to overthrow the Tokugawa Shogunate. Allying himself with the Imperialists, he quickly becomes a hardened killer, and becomes feared far and wide as "Hitokiri Battōsai." After killing another skilled assassin, Kenshin meets a beautiful woman named Tomoe. He contemplates killing her (for witnessing his actions), but instead decides to take her to the Inn where he is staying. Over time, Tomoe and Kenshin grow close to each other once Tomoe realizes how tortured Kenshin is internally over his occupation as an assassin.

Kenshin and Tomoe hide in the remote village of Otsu posing as a married couple in order to avoid suspicion. Months later, Tomoe's brother, Enishi, comes to visit their house and secretly reveals to her that the Shogunate agents are assigned to kill Kenshin. Realizing that she has fallen in love with Kenshin, Tomoe leaves the house while he is asleep in an attempt to deceive the forces into giving up their pursuit of the Battosai.

After Tomoe's disappearance, Kenshin is visited by a comrade who tells him that Tomoe is a spy they were looking for (unaware that the true spy is his comrade). While on his way to find Tomoe, three Shogunate agents ambush him. Outnumbered, he becomes badly injured due to his distressed mental state. Just before the agent's leader can deal the final blow, Tomoe steps in between the two to protect Kenshin, but in doing so receives a fatal injury. Devastated by Tomoe's death, Kenshin vows to never kill again in honor of her life.