Kaoru makes Kenshin stay in the separate room because he saw her naked when she was taking a bath. He was trying to ask if she was OK but thought she was quiet because she was trying to kill herself.(reason= her last students quit) Also near the end of the episode when Kaoru invited Kenshin to stay with her, he said that he might see her naked again. She punched him and apologized because she thought he could dodge it seeing he is the Battousai.
After nearly being pick-pocketed by the young street urchin Myojin Yahiko, Kenshin takes sympathy on the boy who declares himself to be from a samurai family. After his mother's death, Yahiko has been forced into working for the yakuza to pay off his deceased mother's debt. Kaoru goes to rescue the boy but finds herself in a perilous situation until Kenshin appears and defeats the yakuza single-handedly. Kaoru then takes Yahiko as her student at Kenshin's prompting despite the reluctance of both of them.
Yahiko is discontent with the teachings of Kamiya-Kasshin-ryū, wanting to defeat his enemies over protecting the innocent. An old acquaintance of Kenshin invites him to join the military.
Hiruma Gohei, a man who Kenshin had previously defeated in episode 1 hires Sanosuke Sagara (aka Zanza after his signature weapon, a zanbato) to take Kenshin down. He accepts, but not for the money.
Zanza returns to fight Kenshin, and reveals his reason for fighting and his past with the Sekihoutai, where his captain and teammates were used as scapegoats by the government. Kenshin defeats him and breaks the zanbatou, and they become allies.
Government officials are being murdered. Jinei, a former hitokiri known for his ruthless attitude, is doing it and the government asks Kenshin for help. When Jinei sees Kenshin, he realizes he has a worthy opponent and kidnaps Kaoru, telling Kenshin to meet him later.
Jinei has kidnapped Kaoru in order to force Kenshin back into his murderous ways. Kenshin almost kills Jinei, but Kaoru calls out, and he spares him. Jinei then takes his own life.
One of Sano's friends has died from opium when a mysterious woman (Takani Megumi) shows up and needs his and Kenshin's help. She is being pursued by the Oniwabanshuu onmitsu, an elite group of ninja that used to protect the Edo castle. They protect her, but Yahiko is poisoned.
Takeda Kanryū forces Megumi to return by threatening the people at the dojo. Sano convinces her to return, but Megumi is captured by one of Kanryū's underlings.
The group goes to retrieve Megumi, but the Oniwaban group stands in their way. Kenshin narrowly defeats Hannya and then he and Sano confront commander Shinomori Aoshi. Aoshi takes out Sano with one blow, and then he and Kenshin begin to battle.
Kenshin narrowly defeats Aoshi. Aoshi asks Kenshin to finish him off, and when Kenshin refuses, Aoshi vows revenge. Kanryū shows up with a gatling gun and kills the four members of the Oniwaban group, who die defending Aoshi. Megumi tries to kill herself for her past misdeeds, but they save her just in time. Aoshi buries his comrades and swears that he will defeat Kenshin for their sake.
Yahiko meets a cute girl named Tsubame, who works at the Akabeko. She's being forced into making a copy of the key to the Akabeko by a group of thugs, and Yahiko decides to help her by himself. He defeats the thugs, although with a little help from the group.
Kaoru takes in Toramaru, a sumo wrestler who has been kicked out of his sumo stable. The leading wrestler fears being overtaken, and uses his status to keep Toramaru down. Kaoru teaches Toramaru to be self confident, and he rejoins the sumo stable.
Megumi treats a girl with a life threatening heart condition, but a faith healer enters town and begins to seeminly perform miracles to cure the sick at exhorbitant sums, while spreading rumors that Megumi is a quack. When the young girl is put in a life threatening situation because of her parents' desperation, the Kenshin-gumi rush to save her before it's too late.
The Jinpuu squad is performing vigilante assassinations. They try and force Sasaki, a local schoolteacher, to pick up his sword again, but Sano and Kenshin fight them off. Toma, the Jinpuu leader, vows to kill Kenshin.
Toma was a former student under Sasaki. Ultimately, the Jinpuu squad is taken down and Toma repents to his former master.
The group goes to the circus and Yahiko takes a liking to the "Human Cannonball" girl Marimo. A circus boss tries to sabotage the show and make Marimo work for him, but the Kenshin-gumi entertain the crowd until Marimo can find the right mix of gunpowder and fly from the cannon.
Hiruma Gohei returns and hires the Onizaki brothers to kill Kenshin. Gohei tricks Yahiko into bringing him the reverse blade sword, and then he ties Yahiko up. Kenshin is outmatched by the Onizaki brothers, but Yahiko escapes and brings the sword, allowing Kenshin to win.
The Kenshin-gumi go on vacation in Izu. There, a wealthy boy Yutaro falls under the influence of Raijuta, who intends to create a kingdom with his warriors. Kenshin battles Raijuta's men for the sake of Yutaro, but they gain the upper hand.
Kenshin leaves Raijuta's warriors to save Yutaro from drowning. Kaoru teaches Yutaro the Kamiya Kasshin style of swordsmanship, although he doesn't understand its moral aspects. The military attacks Raijuto and his gang.
Kenshin stops the battle by challenging Raijuta to a one on one battle. He figures out the trick to Raijuta's vacuum cut, and defeats him. Yutaro is injured in the battle, and decides to move to Germany for better medical care.
The Kenshin-gumi take a train trip to Yokohama for fun. A train robbery ensues, and they defeat the robbers. All the while, Sanosuke complains technology is the work of the devil.
Sanosuke goes to a picture shop to buy a picture for Miss Tae at the Akabeko. While at the picture shop, he stumbles across a portrait of Captain Sagara, drawn by Tsunan Tsukioka, another surviving member of the Sekihoutai. Sano joins with Tsunan and defeats Tashiwachi Shindo, the man who framed Captain Sagara ten years earlier.
Sanosuke throws a party at the Kamiya Dojo for everyone. Little does everyone except Kenshin know, Sanosuke is really planning to leave the Kenshin group for good to revive the long lost Sekihoutai with his friend Katsuhiro. Kenshin goes to stop Sanosuke and Katsu from destroying the Internal Affairs Department with bombs. Kenshin stops Sano, and Sano rejoins Kenshin's group, and Katsu stops making bombs.
The Crimson Pirate: Kenshin and Kaoru, Seperated!
In this episode, Kaoru finally gets fed up with Kenshin, Yahiko, and Sanosuke hanging around the Kamiya Dojo, without working or paying any money to help her feed everybody. They feel bad, and go out looking for a job to help pay their way. They sign up for a team of warriors that have been hired to capture the Kairyu pirates, a group of freakish rouges that have been raiding silk ships on the high seas. On the cruise, they come across Kaoru, who has also signed up to raise money for the dojo. They're surprised to see each other, and Kenshin is worried about Kaoru's safety. The Kairyu pirates are known for their violence, and some even go as far as to call them demons. Their leader, Shuura, is a ruthless masked figher with nunchaku.
During the night, Kenshin is out getting some air. Kaoru comes out, and they share a small moment. It's interrupted, however, when they see the Kairyu pirates approaching. Everyone inside is alterted, and th
Shura and the Kairyu land at Kairyu Island with Kenshin. Shura doesn't have the heart to kill Kenshin, and so Ginjo, one of the Kairyu who wants to be the new leader instead of Shura, makes up a plan to kill Shura and become leader in her place. Shura gets shot in the leg by Geki, another one of her followers who has now joined Ginjo.
Kenshin helps to nurse Shura back to health, then Shura finds out that Ginjo gave Old Iwa opium. Shura goes off to fight and defeat Ginjo. She is defeated by him, since he played a dirty trick on her. Kenshin then comes in and uses the Ryu Tsui Sen to end the fight. Geki then throws a bomb, destroying Kairyu Island and all its inhabitants, except for Kenshin and Shura.