In the year 1878, during the early Meiji era, former hitokiri Himura Kenshin has found a measure of peace living at the Kamiya Kasshin-ryu dojo in Tokyo with Kamiya Kaoru, Myojin Yahiko, and Sagara Sanosuke. This quiet life is shattered when Home Minister Okubo Toshimichi, a powerful figure in the new government, seeks Kenshin out with an urgent request. He reveals that Makoto Shishio, Kenshin's successor as a government assassin during the revolution, is still alive. Betrayed and left to burn to death by the leaders he served, Shishio survived, his body horrifically scarred and wrapped in bandages. Now consumed by a desire for revenge against the Meiji government, he is gathering a powerful army in Kyoto with plans to overthrow the new regime and rule Japan himself.

Kenshin initially refuses to leave his new life and break his vow never to kill again, but when Okubo is murdered in broad daylight by Shishio’s unnervingly polite and exceptionally fast young right-hand man, Seta Sojiro, Kenshin realizes the threat is inescapable. He bids a painful farewell to Kaoru and departs for Kyoto. Along the way, he meets the spirited young thief Makimachi Misao, who is trying to steal his reverse-blade sword, and through her he is introduced to the Oniwabanshu, a group of former shogunate spies now running an inn in Kyoto. Their leader, Okina, warns Kenshin that another dangerous man, Shinomori Aoshi, is also hunting for him, seeking to prove his strength.

Kenshin’s journey to confront Shishio is a gauntlet of battles. He is confronted directly by Shishio, who orders Sojiro to duel him. In this fight, Sojiro’s incredible speed and skill lead to Kenshin’s trusted sakabato being shattered. With his iconic sword broken, Kenshin travels to the remote village of a legendary swordsmith, Arai Shakku, only to find he has died. Shakku’s son, Seiku, has abandoned sword-making and refuses to forge a new one. When one of Shishio’s elite warriors, the wild and flamboyant Sawagejo Cho, kidnaps Seiku’s baby to force the issue, Kenshin fights to rescue the child, proving his worth. Seiku then gives Kenshin a new, stronger sakabato, a twin to his original.

Learning that Shishio plans to burn Kyoto to the ground in a massive fire, the government police, led by Kenshin’s old ally Saito Hajime, join forces with Kenshin and the Oniwabanshu to defend the city. They are aided by Sanosuke, Yahiko, and a worried Kaoru, who have followed Kenshin to Kyoto. While they manage to thwart the attack on Kyoto, Kenshin realizes it was a diversion. Shishio’s true target is Tokyo. Rushing to the harbor, Kenshin confronts Shishio on his ironclad warship. In a brief but intense clash, Kenshin fights the powerful Shishio but is unable to defeat him. The battle ends in tragedy when Sojiro throws Kaoru overboard into the dark sea. Kenshin, in a moment of despair, dives in after her. The film concludes with Kenshin washed up unconscious on a distant shore, his fate and Kaoru’s unknown, as a mysterious figure approaches to carry him away, setting the stage for the final confrontation.