The Legend Ends opens immediately after the events of Kyoto Inferno, with Kenshin Himura washed ashore and discovered by his former master, Hiko Seijuro. Unconscious and near death after his previous confrontation with the villainous Shishio Makoto, Kenshin awakens at his master's remote home, having been separated from Kaoru Kamiya during the struggle at sea.

The film follows two parallel paths. Kenshin, believing Kaoru may be dead, begs his master to teach him the ultimate technique of the Hiten Mitsurugi sword style, the Amakakeru Ryu no Hirameki, believing it is the only way to defeat Shishio. Hiko initially refuses, seeing that his student has lost the will to live and carries a reverse-blade sword that reflects his vow never to kill again. Through a brutal training regimen and philosophical confrontation, Hiko forces Kenshin to realize that valuing his own life is essential to mastering the final technique.

Meanwhile, Shishio Makoto has set sail for Tokyo aboard his massive ironclad battleship, the Purgatory, carrying Kaoru as his captive. He demands that the Meiji government turn over the assassin Battosai, Kenshin's former identity, threatening to expose the government's dark secrets from the Bakumatsu era if they refuse. The government, led by Home Minister Ito Hirobumi, reluctantly brands Kenshin a wanted criminal and schedules his public execution. Shishio's men attend the execution to ensure the government follows through.

The execution, however, proves to be a staged deception. With the help of Saito Hajime, Kenshin is freed, and together with Sanosuke Sagara, they board Shishio's ship. Before reaching Shishio, Kenshin must confront Seta Sojiro, Shishio's young and lethally fast protégé, in a rematch that tests Kenshin's resolve and skill. Shinomori Aoshi also reappears, still seeking to defeat Kenshin, though Misao's intervention leads to a shift in his loyalties.

The final battle pits Kenshin against Shishio in the ship's hold, with Saito, Sanosuke, and eventually Aoshi joining the fight. Even together, the four warriors struggle against Shishio's overwhelming power. Shishio suffers from a critical weakness, his body cannot regulate temperature due to being burned alive years earlier, limiting him to fifteen minutes of intense combat. As the battle reaches its peak, Shishio's body begins to overheat. Yumi Komagata, his lover, attempts to shield him and is killed. Kenshin finally defeats Shishio using the Amakakeru Ryu no Hirameki, not by cutting him down but by forcing his body to its fatal limit. Shishio bursts into flames and burns to death as the government fires upon the ship, intending to sink it with everyone inside.

The group escapes the burning vessel and returns to shore, where Kaoru, having been found alive and unconscious at a hospital, waits with Yahiko and Misao. Ito Hirobumi officially declares Battosai dead while acknowledging Kenshin Himura as a hero. Aoshi returns to Kyoto with Misao, while Kenshin, Kaoru, Yahiko, and Sanosuke go back to the Kamiya Dojo. Kenshin expresses his desire to continue living in the new era, setting aside his past as an assassin and moving forward alongside Kaoru.