Kenshin, Kaoru, and Yahiko visit Akabeko, a beef hot-pot restaurant, where a group of democratic rights activists gets into a heated argument. One of them throws a bottle of sake, and it hits Kenshin, causing a commotion. Sanosuke Sagara, who happened to be in the store during the quarrel, stood up and blew away the activists with a single flick to the forehead. Seeing Kenshin's strength, Sanosuke's curiosity is roused and he asks, "You wanna buy a fight from me?"

Sanosuke's friend has died from an opium overdose. However, Kenshin and Sanosuke are perplexed at how he even got his hands on the drug, since opium is banned and too expensive for the average person to afford. Then a mysterious woman, Megumi Takani, appears before them. Kenshin and the others fight off Kanryu Takeda's private army who is trying to capture Megumi. However, Megumi is carrying opium...

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 and the group are enjoying some tea time together. The group probes Kenshin to entertain them with an interesting story from his travels, specifically requesting "a story that's unusual, fun, and includes a villain's defeat." To answer to their demands, Kenshin decides to tell them about someone he met when he was visiting a foreign settlement in the lively city of Yokohama. A foreign doctor named Elder who was always wearing a mask.

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 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.

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.

Kenshin reunites with Kaoru and the rest at Seijuro Hiko's place, who is a master of Hiten Mitsurugi-ryu. Seijuro learns from Kaoru that Kenshin goes around the country acting as a rurouni who helps people, when he then decides to pass down the last ultimate technique of the Hiten Mitsurugi-ryu.

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

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.