Raijuta, who wants to revive the murderous sword, considers Kenshin, who denies his idea, as an enemy. Raijuta initiates a fight using his actual sword, but Kenshin lands a blow that breaks Raijuta's sword and stops the situation from escalating further. After some time has passed, Yutaro, a boy who claims to be Raijuta's apprentice, arrives at the Kamiya Dojo. He claims he has come to challenge Yahiko, with whom he doesn't get along, to a match, but the way Yutaro holds his bamboo sword is no good...

Tsunan is seeking to clear his decade-old unresolved regrets surrounding the Sekiho Army. Empathizing with him, Sanosuke joins Tsunan in conspiring an attack on the Home Ministry. However, Kenshin was waiting for them inside the building to stop them. Seeing the former Revolutionary warrior standing in their way, the same way they faced off against Revolutionary warriors when they were in the Sekiho Army, Tsunan's fighting spirit burns. A flurry of explosives are hurled at Kenshin.

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...?

The name of the girl that Kenshin encounters in the forests is Misao Makimachi, and she came from Kyoto to find Aoshi’s Oniwaban Group. Kenshin is surprised to hear his name. Upon seeing Kenshin’s reaction, she asks him if he knows where Aoshi is, but he keeps his mouth shut. However, Kenshin is touched by the emotions Misao has for Aoshi, in which he then decides to make the journey to Kyoto with her.

Kenshin defeats Senkaku and finally faces off against Shishio. However, Shishio expresses his disappointment at Kenshin's policy of refusing to kill and lets his close associate, Sojiro Seta, deal with Kenshin. He leaves the village with another associate of his, Yumi Komagata. To continue his pursuit of Shishio, Kenshin faces off with Sojiro and exchanges blows of Battojutsu, which can make or break the fight's outcome. It is a battle of divine speed from both sides...

Seeking a replacement for his broken sakabato, Kenshin visits Seiku, the son of highly honored swordsmith Shakku Arai, only to learn that he has quit making swords. Respecting Seiku’s philosophy of peace, Kenshin gives up his request for a new blade. Meanwhile, Ten Swords member Hoji Sadojima reports to Shishio on Kenshin’s movements.

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.

Aoshi injures Okina, leaves Misao behind, and shows up at Aoiya. He asks the Oniwaban Group where Kenshin is. Aoshi's in a ghastly state, but accepts what Yahiko and Kaoru tell him and decides to wait for Kenshin where Shishio is. Okina is on the verge of death but undergoes treatment by Megumi, who has come rushing to Kyoto.

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.

It is now midnight. Goichi and the others start moving as it is time to put the Great Kyoto Fire plan into action, when they witness Shishio's other underlings being chased by the police. Henya is annoyed that the fires haven't started on time. Meanwhile, an order is dispatched to the Ten Swords, and they start moving upon hearing their orders. Behind the scenes, Kenshin and the rest arrive at Osaka Bay only to come across something.

The engine room of Rengoku. Hoji manages to catch the explosives and prevents the room from blowing up. However, Sanosuke delivers the Mastery of Two Layers to the ship's Kingston valve, flooding the perimeter. Meanwhile, Usui reveals himself to Kaoru, Yahiko, and Misao as Arato faces off against Kamatari and Henya. Goichi begs for Megumi's help at her clinic to heal Tokuji, his younger brother. As these passions clash with each other in all places of Kyoto, a small, over-looked fire begins to flare up.

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.