While a raid of bandits slay a group of travelers, a young boy named Shinta is saved from death by a passing swordsman. The swordsman, known as Hiko Seijūrō, is a master of the Hiten Mitsurugi, the strongest of all sword forms. Hiko takes Shinta as an apprentice and renames him "Kenshin", a name which he felt was more appropriate for a swordsman.
After years of training, Kenshin leaves his master, convinced that the only way to uphold the Hiten Mitsurugi's pledge to help the weak and innocent is to join the revolution poised to upend the Tokugawa shogunate. He joins the Choshu clan and soon works for their leader, Katsura Kogorō, as an assassin. Kenshin soon becomes a hardened killer, feared far and wide as the Hitokiri Battōsai. During a successful assassination, he kills a bodyguard named Kiyosato Akira. The encounter with Kiyosato leaves Kenshin with the first half of his cross-shaped scar. After killing a skilled assassin, Kenshin meets a woman named Yukishiro Tomoe, unaware of the fact that she is the fiancée of Kiyosato. Kenshin takes her to the inn where he and the men of the Choshu clan are residing. Katsura suspects a spy among the Choshu after Kenshin informs him of the assassin he killed.
After the Ikedaya affair, Katsura arranges for Kenshin and Tomoe to hide in the village of Otsu as husband and wife, so the two would not be suspected. After a few months, Tomoe's brother Enishi comes to visit and secretly reveals to his sister that the shogunate agents assigned to track down and kill Kenshin are close by, and that her revenge will be complete. Tomoe sends Enishi off, feeling ill at ease. It is here that Tomoe realizes that she has fallen in love with Kenshin. Kenshin, too, is in love with Tomoe. The next morning, Tomoe leaves the house and tries to deceive the shogunate men into giving up their pursuit of Kenshin and unsuccessfully attempts to kill their leader.
After Tomoe's disappearance, Kenshin is visited by a comrade who tells him that the spy was Tomoe and that she is meeting at that moment with her co-conspirators. He also reveals to Kenshin that she is the fiancée of Kiyosato, the man he killed. Kenshin, however, is unaware that it is this man who is the real spy. While heading to Tomoe's location, a heavily-shocked Kenshin faces and kills three of the four shogunate agents but becomes badly injured due to his traumatized state. While Kenshin is fighting with the last agent (a fist fighter), Tomoe steps in between the two to protect Kenshin from the killing punch. This allows Kenshin to kill the agent but, in doing so, unintentionally impales Tomoe also. Before her death, she gives him the second part of his cross-shaped wound.
Kenshin, blaming himself for Tomoe's death, swears to fight to bring about the age desired by Katsura, but after that to continue fighting to protect the innocent without killing again. Katsura informs Kenshin that he had a new assassin kill the real spy. As the Tokugawa shogunate is nearing its end, Kenshin has his first encounter with the Shinsengumi captains Okita Sōji and his future rival, Saitō Hajime. It is then revealed that once the Bakumatsu revolution had ended, the Hitokiri Battōsai had disappeared without a trace. Then Kenshin returns to the graves of the women he buried when he was a child and places Tomoe's scarf on them. Sometime afterwards, Hiko Seijūrō returned to the site and notices the scarf, realizing Kenshin had returned and he had barely missed his former student.