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...

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.

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.

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.

Kenshin, Sanosuke, and Yahiko scramble to take back Megumi from the Kanryu residence. They are confronted by Han'nya, a spy of the Oniwaban Group. He trifles Kenshin with his martial arts skills and his "Arm-extension Spell", but Kenshin successfully conquers him when he uncovers the secret of the technique during the fight. Just when it looked like the battle was up, Han'nya removes his mask and reveals his startling true face.

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.

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.