Kenshin confronts Sanosuke, who wields the giant Zanbato with ease. However, Sanosuke shows his incredible durability after withstanding a strike from Kenshin with ease. This leads Kenshin to instead launch a barrage of blows at him, and Sanosuke falls to the ground. For a moment it looked as if victory has been decided. However, while Sanosuke is in a daze, he recalls the reason for his obsession with victory, his past from ten years ago when he was in the Sekiho Army...

Kenshin receives a request from the police chief, asking for his help to take down "Kurogasa," a serial killer who has been repeatedly targeting former Revolutionary warriors. Kenshin and Sanosuke go to escort Jusanro Tani, who received a letter containing a death threat. As warned in the letter, at 1:00 a.m. sharp, Kurogasa appears. His true identity was Jine Udo, a vagabond slayer who had made a name for himself in the assassination business since the Bakumatsu Era.

At last, Kenshin faces off against Aoshi Shinomori, the head of the Oniwaban Group. In the Bakumatsu Era, the battle-obsessed "Oniwaban group" lost their meaning of existence after surrendering the castle they served without even being able to fight. Aoshi is unable to bear this regret and is in earnest pursuit of the title of the strongest warrior. As a former Revolutionary warrior, Kenshin cannot tolerate conflict without morality. Two men who made killing their profession in the Bakumatsu Era clash against one another, putting their pride on the line.

Yutaro sustains a heavy injury from Raijuta's sword, and it is so severe that he will never be able to swing a sword with that arm ever again. Although Yahiko was constantly disagreeing with Yutaro until now, he understood very well what swordsmanship meant to him. He takes Yutaro's hand and leads him out of the medical room, so they could witness the final battle between Kenshin and Raijuta.

Deep in the night on a woodland path, Kenshin and Raijuta's duel begins.

Kenshin sees a dream recalling the Shinsengumi, who he faced off against back when he was a Revolutionary warrior. The Shinsengumi was a group of highly skilled swordsmen who he fought on equal footing back when he was the Hitokiri Battosai. He feels unsettled and ponders why he is suddenly remembering them. As the tension persists, a mysterious man with very unique-looking eyes pays a visit to the Kamiya Dojo while Kenshin, Kaoru, and Yahiko are not home. When he meets Sanosuke, who just happened to be at the Dojo, he claims that he is Goro Fujita, a medicine seller, but...

The person who had sent Hajime to face Kenshin was none other than the Head of the Home Ministry, former Satsuma Domain Revolutionary warrior, Toshimichi Okubo. He asks Kenshin to go to Kyoto to stop the secret plans of a man who claims to be the legitimate successor of the Hitokiri Battosai. However, that man was supposed to have been killed 10 years ago by his own comrades in the government, as they regarded him as a threat. Receiving this request to conduct an assassination, what will Kenshin's answer be...?

Kenshin steps into Shingetsu Village, a place where the Mishima brothers escaped from. The village is currently under the control of Senkaku, Shishio’s subordinate, who rules with an iron fist and uses violence to control the villagers. They are frightened of the violence and unable to do anything but obey. The village has decayed and exudes an unusual aura about it. Kenshin heads over to where Shishio is located with Hajime, who’s learned about the current situation and visited the village. In the background of these events, Eiji’s heart burns with the desire for revenge against Senkaku.

Known as “the Sword Hunter” in the Ten Swords organization, Cho is adept at maneuvering a variety of different and unique swords. As for Kenshin, he continues to risk his life and fight for peace in the new era and to save Seiku’s son, Iori, even though he’s forced to fight with a broken sakabato.

Kenshin obtains a new sakabato. Having involved Seiku in this conflict, he decides to leave Aoiya before inviting any further danger. Meanwhile, Misao stops by Shirobeko, a beef hot-pot restaurant where Kaoru and Yahiko work part time, where she learns Kaoru is searching for Kenshin.

Kenshin undergoes training so that he can learn the ultimate technique. He barely manages to get in a hit against Seijuro in a bout, where he then learns "Kuzuryuusen,"a powerful technique that launches nine slashes at the same time. Kenshin learns to see through Seijuro's swift sword movements and masters "Kuzuryuusen" by looking at it only once. However, the technique was only born out of the process of passing down the ultimate technique, "Amakakeru Ryuu no Hirameki" of Hiten Mitsurugi-ryu.

Kenshin and Aoshi engage in a battle on the deck of the ironclad Rengoku. Behind the scenes, Sanosuke manages to board the ship and tries to blow up the engine room with the explosives he got from Tsunan. However, Shishio's underlings Hoji, Shuzo, Toshiro prevent him from going any further. Meanwhile in Kyoto, Arato faces off against Kamatari and Henya alone to buy time for the police forces to evacuate.

Shishio sends a dueling challenge directed at Kenshin, Hajime, and Sanosuke. The duel is to be held the next day on Mt. Hiei, northeast half way up the mountain in a small shrine with a six-storied torii. At Shishio's fortress, Hoji proposes a strategy to Shishio for an "absolute victory," when the Ten Swords assemble there.... And on the night before the duel, Kaoru talks to Kenshin as he stares up into the night sky.