Making the decision to fight against Shishio, Kenshin leaves Kamiya Dojo and sets off for Kyoto via the Tokaido by himself. Meanwhile, Sanosuke and Yahiko attempt to go to Kyoto to follow Kenshin.

Megumi is alone in Tokyo and coincidentally encounters Aoshi at Kamiya Dojo, who's come back for another fight with Kenshin. Aoshi asks Megumi where Kenshin is, but she feigns ignorance. Unhappy with the lack of response, he threatens to kill her if she doesn't tell him, when a man suddenly appears. Meanwhile, Kenshin encounters a young girl in the forests of the Hako...

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 ...

Kenshin enters Shingetsu Village, now ruled by Shishio's violent subordinate Senkaku. The terrified villagers submit as the place decays. With Hajime, Kenshin seeks Shishio while Eiji yearns 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 Ba...

Lost in the forest en route to Kyoto, Sanosuke meets monk Anji who shows him a powerful strike. Anji offers to teach him the "Mastery of Two Layers" with one month to learn it or die. Sanosuke boldly claims he'll master it in a week.

Kenshin and Misao arrive in Kyoto, where they're welcomed by Okina, a grandfather figure to Misao. It turns out, Okina is a former member of the Oniwaban Group. Okina offers his help and Kenshin ask him to help find someone for him.

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.

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 is suffering from a high fever in a shrine. Sensing some disturbance he puts his guard up. The hunters leave, and Kenshin falls asleep. When he awakens, he finds himself being nursed by Giichi and his wife Satsuki in their home.

Kenshin obtains a new sakabato. Having involved Seiku in this conflict, he decides to leave Aoiya before inviting any further danger.

Kenshin meets Kaoru at Seijuro Hiko's home. Seijuro, master of Hiten Mitsurugi-ryu, hears of Kenshin's wandering life helping others. He decides to teach Kenshin the style's final, ultimate technique.

Hoji deploys the Owl Clan to attack Aoiya and capture Okina, seeking info on Kenshin. The plan fails, with the Owl Clan defeated. Okina then challenges Aoshi to battle through a captured clan member.

After the battle between his loved ones broke out, Misao makes a decision in the face of Okina's near death, to finally defeat Aoshi.

Kenshin suffers an extremely intense duel against his teacher, in order to give him a blow and thus learn the supreme technique of the Mitsurugi style.

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.

Kenshin and Hajime discover Shishio's Osaka plans. Meeting Sanosuke, Kenshin sends a letter to Aoiya for help against the Great Kyoto Fire, with Arato supervising. They head to Osaka Bay when Officer Omi brings young Kitazawa to meet Arato.

Police and people in Kyoto, led by Misao, prevent fires. Meanwhile, Kenshin and Shishio face each other at Osaka port.

Kenshin's group clashes with Shishio's faction to protect Kyoto. Kenshin fights Aoshi on Shishio's ship while Sanosuke tries to blow up the engine room, opposed by Hoji.

Sanosuke finds the Purgatory battleship's engine room, but Hoji blocks his way. Explosions make Shishio postpone the final battle. In Kyoto, Usui and Anji fight as Kaoru, Yahiko and Misao watch in bewilderment.

In Kyoto, Kaoru quickly notices something strange with Misao, as Misao comes back to the location where a fire was put out. At Megumi's clinic, Omi awakens, bringing tears of relief to Juro. Meanwhile, a black tag is put on Tokuji's toe to mark that he is dead. Kenshin and the others come back to Aoiya, where they learn from Omasu that Okina has woken 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 ...