It's been a week since the resolution of the crossroad killing case, in which the name of the Kamiya Kasshin-ryu was deceptively used. Although the name of Kamiya Dojo has been cleared, there's no sign of an increase in the number of Kaoru's students. Then a passing boy, Yahiko Myojin, pickpockets Kenshin's wallet. Kenshin gives him the wallet, saying that it was his fault for allowing it to get stolen. Yahiko is repulsed at being treated like a child, but he has a reason to collect the money.

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.

The pursuers from the Oniwaban Group haven't made an appearance for over a week, and during this time Megumi familiarized herself with the Kamiya Dojo group. Sanosuke, however, was still unsettled and feeling frustrated knowing that Megumi was the one who made the opium that caused his friend's death. Then one day, Megumi suddenly disappears. In a letter they found from her, it stated that she had left of her own volition, but Kenshin and the others found this to be unnatural. They decide to head to Kanryu Takeda's residence, the man who was sending spies after her.

Kaoru, Kenshin, and Yahiko visit Maekawa Dojo for a training session. The dojo is very lively, and Kaoru's training is well-received by the students of other sword styles. Then a swordsman named Isurugi Raijuta breaks in. He says he is concerned about the future of sword art, and the man, carrying only an actual sword, dismisses the idea of a bamboo sword match. In order to defeat the challenger, Maekawa, the master of Maekawa Dojo, takes on Raijuta, but...

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.

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...

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.

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.

Going back in time, the 4th year of Keio. Kenshin is suffering from a high fever in the main hall of a desolate shrine. Kenshin falls asleep and when he awakens, he finds himself being nursed back to health by former private detective Giichi and his wife Satsuki in their home.

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.

As a result of passing down the ultimate technique, Seijuro endures a fatal wound.

Shishio's underlings inconspicuously prepare for their battle plan when patrols arrive causing them to retreat.

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.