The movie starts with a short backstory from Kenshin’s childhood. Hiko Seijuro found the little boy digging up graves for the corpses lying around him. (Those were the bodies of the slaves that were ambushed by bandits. The bandits were killed as well by Seijuro who saved Kenshin.) Seijuro renamed the boy from Shinta to Kenshin, which, according to him, was more fitting for a swordsman. He took him in and trained him for several years under his guidance and teachings.
The scene is cut and Himura Kenshin abruptly rises from his sleep after dreaming about his past. He goes outside and is surprised to see his former master, and there, the two of them updated each other about their lives after their separation. He pleads his master to teach him the ultimate technique of Hiten Mitsurugi-ryū to be able to defeat Shishio Makoto. After exchanging blows several times, Hiko Seijuro finally teaches Kenshin the succession technique after the latter realizes the significance of his life and his will to live. Right after that, Makimachi Misao arrives and assures Himura that Kaoru is alive while warning him about the government’s scheme. Ito Hirobumi, one of the prominent figures of the Meiji government, is coerced by Shishio to find Battousai and execute him in public. Hence, Himura Kenshin becomes the scapegoat of the government and declares him as a wanted criminal in Japan.
Kenshin goes back to Aoiya Inn with Misao and they find out that Okina is gone. The old member of Oniwaban group tries to stop Aoshi Shinomori for the last time despite the grave wounds on his frail body. Just as he clings on to Aoshi desperately, Kenshin arrives there together with Misao and the other Oniwabanshū member. Aoshi finally meets him and they immediately start to duel. After the breathtaking fight, Kenshin emerges as the winner while Aoshi is left severely injured. Kenshin doesn’t kill him even though Okina instructed him to do so. Misao takes Aoshi to the inn and tends to his wound after mourning the death of the elder Okina.
Kenshin stops by the Kamiya dojo and chances upon Takani Megumi who is currently looking after the residence. However, the police officers arrive and arrest Kenshin who eventually surrenders himself to avoid further dispute. He is then brought before Ito and after he assures him that he can defeat Shishio, they both frame a plan to enable Kenshin to get closer to his enemy. Their idea is to pretend as if he will really be decapitated in public just like what Shishio wants. Kaoru, Yahiko and Sanosuke, who have no idea about the plan, all show up at the execution site. They immediately go there after Kaoru was confined to the hospital where she was brought by the fishermen who saved her. To everyone’s surprise, instead of getting beheaded, the executioner, who turns out to be Saito Hajime, severs the ropes that tie Kenshin. That instance, a battle ensues between the police officers and Shishio’s henchmen, including some members of Juppongatana. (Unfortunately though, the duel between Saito and Usui that we have all been looking forward to is reduced to a brief encounter where Saito easily cuts through Usui.) Sanosuke accompanies Kenshin on his way aboard the Rengoku (Shishio’s ironclad battleship) while Kaoru and Yahiko are left at the site.
Several police officers also get on the ship to provide aid and assistance to the other two. Sanosuke, on the other hand, comes across a fallen Buddhist monk named Anji and gets critically injured despite his victory against his enemy. Meanwhile, Seta Sojiro greets Kenshin and the two immediately begin fighting. Sojiro manages to be on par with him at first but is later put at a disadvantage when he gradually starts showing his emotions, enabling Kenshin to defeat him. Sojiro has lived by the rule of Shishio Makoto, where he believed that “the strong live and the weak die”, and after being beaten by the Battousai, he starts to question himself and the decisions he has made. Kenshin tells him to spend his life seeking for the truth to enlighten himself, and the parting words that he gives him cause Sojiro to become deranged and unstable.
As Kenshin wanders inside the ship, he is welcomed by Hoji and his Gatling gun. However, Hoji is stopped by Shishio Makoto, and the Juppongatana leader finally confronts his predecessor. And at long last, the battle between the two hitokiri commences.
At first, it is clearly apparent that Shishio is stronger than the Battousai, especially after that epic scene where he bites Kenshin on the shoulder and hurls him to the ground. That instance, Saito Hajime appears and Shishio fights him as well. His Gatotsu technique doesn’t seem to affect Makoto at all. In the middle of their duel, Sanosuke Sagara arrives and meddles in their fight but is also easily overpowered by the enemy. When both Saito and Sanosuke are cast aside, Shishio tries to attack Kenshin once again but is abruptly stopped by Aoshi Shinomori, who claims that he will be the one to defeat Kenshin. The four of them attack Shishio simultaneously while the latter flares his Mugenjin (Infinity Blade) which literally enables him to execute fire-oriented techniques. As the battle comes to its peak, only he and Kenshin remain on their feet, both exhausted from the gruelling combat. At one point, Shishio falls on his knees, and as Kenshin readies himself to deliver the final blow, Komagata Yumi, Shishio’s lover, stops Kenshin in his track. She pleads him to cease the fight since Shishio’s body can no longer withstand the abnormal rise of his body temperature. The doctor informed him earlier that he can only fight for a maximum of 15 minutes, since his sweat glands were burned and his body heat is higher than the normal level. And to Kenshin’s surprise, Shishio mercilessly pierces Yumi with his sword, impaling Kenshin in the process. He is utterly startled at how Shishio desires to kill him at any costs, even at the expense of Yumi’s life. However, Shishio refutes that she died happily knowing that she became of great use to his most important battle. He also asks the lifeless body of Yumi to wait for him in hell as he continues to fight Kenshin even if he already spits blood. Kenshin delivers his ultimate technique—the Amakakeru Ryū no Hirameki that his master Seijuro taught him. The technique proves to be extremely powerful as it slashes across Shishio’s body, which signals the end of their battle. After carrying Yumi’s body next to him, Shishio Makoto sends his farewell to his predecessor as his whole body combusts. His sinister laughter is heard while his body is surrounded by raging flames. Sanosuke supports Kenshin on their way to escape the collapsing battleship together with Aoshi and Saito.
As their boat reaches the shore, they are welcomed by Kaoru, Yahiko, Misao and Ito’s soldiers. Just as when they thought that Ito will still execute Kenshin even after knowing that he already defeated Shishio, Ito Hirobumi commands his soldiers to salute Himura Kenshin. Kamiya Kaoru then helps him walk and welcomes him home.
Back at the Kamiya dojo, Kenshin is seen viewing the serene surroundings while sipping his tea. Sanosuke is cooking and Yahiko is practicing kenjutsu with the new students. Kaoru sees Kenshin and sits next to him as they chat. Kenshin then stands up and picks a maple leaf and hands it to her. The movie concludes with Kenshin’s roundabout-like-proposal to Kaoru, asking her to continue watching over the new age with him, as he successfully puts an end to Shishio but most importantly, to the legend of Hitokiri Battousai that existed within him.