11th year of the Meiji Era in downtown Tokyo. Kaoru Kamiya, the acting master of the “Kamiya Kasshin-ryu” style, was chasing after the “Hitokiri Battosai,” who was claiming to be a user of her sword style. One night, Kaoru meets a man carrying a sword. She immediately questions the man, but he seems to have absolutely no will to fight. “Is this the rumored Hitokiri Battosai?” As Kaoru dubiously looks on, the man introduces himself as Kenshin Himura, a “Rurouni.”

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.

Yahiko's heart is moved by Kenshin and he decides to quit pickpocketing. Yahiko refuses to pay Kanto Shueigumi and resists their demands, but he is beaten up. Kenshin comes to his rescue and settles the matter. Regretful that he could not solve the problem by himself, Yahiko wishes to become stronger. Seeing this, Kenshin takes Yahiko to the Kamiya Dojo.

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?"

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...

Knowing how strong Kenshin was when he was the Hitokiri Battosai, Jine takes Kaoru hostage in order to fuel Kenshin's anger. The two engage in a fierce battle. However, Jine, believing that Kenshin has not yet regained his former strength, inflicts the Nikaido Heiho "Shin no Ippo" on Kaoru, causing her to stop breathing. With only two minutes until Kaoru dies of asphyxiation - Kenshin's anger reaches its peak.

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...

Hyottoko, a member of the Oniwaban group, raids Kamiya Dojo, where Megumi is hiding. He unleashes his special attack "Fire Breath," in which he breathes fire from his mouth, onto Kenshin and Sanosuke. Anticipating the defeat of Kenshin and the others at the appearance of the powerful middle-ranked spy, Megumi tries to flee the scene, but Kaoru stops her and says "He's fighting for you," telling her to believe in Kenshin's strength.

Sanosuke is visiting the sukiyaki restaurant Akabeko, where he always leaves his bill on a tab. One of Akabeko's workers, Tae, asks him to go buy a Nishiki painting from the painting shop on her behalf. Though Sanosuke had no interest in paintings, he finds one at the store that catches his eye. It was a painting of the man he looked up to as his master back when he was a member of the Sekiho Army, Captain Sagara. With a gleam in his eyes, Sanosuke makes his way to meet with the artist of the painting.

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 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...

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 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...?

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 Hakone mountains as he makes his way to Kyoto.

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.

Sanosuke makes his way to Kyoto while trudging through the forest and getting lost at the same time. On the road there, he meets Anji Yukyuzan, a fallen monk currently in training. Sanosuke witnesses Anji unleash an astonishing strike up close, a technique that took Anji 10 years to acquire. There, Anji decides to teach Sanosuke “the Mastery of Two Layers,” an art of destruction. However, he requires Sanosuke to learn the technique within one month; if he fails, he will have to die. Against this unreasonable and excessive condition laid out to him, Sanosuke declares he’ll learn it within a week. The training for this technique, which will make or break his life, begins….

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.

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.

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 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.