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...

In order to kill Kenshin, Kanryu uses his Gatling gun and rains a flurry of bullets at him, uncaring that the Oniwaban Group that was under his command would also be hit by this attack. In the face of this evil act, the Oniwaban Group make full use of their individual abilities to counter the Gatling gun. At this moment, theirs and Kenshin's purpose become one. Kenshin and the Oniwaban group team up to challenge the overwhelming power of a modern weapon.

Yahiko, the sole student of the Kamiya Dojo, has started to step away from his training from time to time. He says he's merely going on a walk, but it is clear that he takes his swordsmanship training very seriously, and it doesn’t look like he's ditching to slack off. Curious about what he's doing, Kenshin, Kaoru, and Sanosuke decide to follow him. What exactly is Yahiko's reason for ditching?

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.

The current Kenshin has left his past as a manslayer and wished for a peaceful world. Though Elder looked at him with eyes of confusion, Kenshin knew that Elder also shared this same desire for a healthy society and felt a sense of comradery with him. Meanwhile, another doctor called Deian Ishizu was scheming to get rid of Elder, as Elder did not seek monetary gain in exchange for her medical services, and Deian thought this was disrupting his business. Deian hires Espiral, a master of Western swordsmanship, to get rid of Elder. However, it seems Espiral has an entirely different motive for taking on the job...

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...

After defeating Arundo Akamatsu, Kenshin returns to the Kamiya Dojo and sees Hajime Saito. Hajime had introduced himself to Kaoru and Yahiko as Goro Fujita, the police officer, and they had invited him into the Dojo without any suspicion. Hajime criticizes Kenshin and the others for their naivety. Over the past ten years that Kenshin had washed his hands of manslaying, Hajime had honed his killing intent and skills as a hitman, and now Hajime's ferocity was aimed at them.

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.

Hoji plans an attack of Aoiya at night using a secret unit, the Owl Clan, in order to capture Okina and catch a hint of Kenshin's whereabouts, but instead the Owl Clan were the ones defeated. Okina challenges Aoshi to a battle via a member of the clan whom he sent back to Shishio's location.

Kenshin and Hajime realize that Shishio has another objective in mind that lies in Osaka. They meet up with Sanosuke there. To stop the Great Kyoto Fire, Kenshin asks for help from everyone at Aoiya via a letter while leaving Ryusaku Arato, the chief of police, in charge of supervising on the ground in Kyoto. Kenshin, Hajime, and Sanosuke head to Osaka Bay on a carriage after they finish their errands. Then, senior police officer, Hikozaemon Omi brings along Juro Kitazawa, a young 11-year-old boy who says he wants to meet with Arato.