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.

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.

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.

While Sojiro is occupied by constantly re-tieing his shoe, he thinks of the moments of his past, and all of the bad stuff that happened in it. Sojiro's past is shown throughout the entire episode. Sojiro's family never loved him, and only wanted him so they could use him. They made him carry hundreds of buckets of rice, and when Sojiro returns a bucket of rice to his house, one of Sojiro's family members breaks the bucket on purpose. Then, another person who likes to cause Sojiro trouble and use him, named Yanosuke, calls out his father who is inside, blaming Sojiro for breaking the bucket. He then meets Makoto Shishio, whom spared his life. Shishio gave him a Wakizashi sword. When his family has cornered him, he murders them with this sword. Then, Sojiro follows Shishio, as Shishio tells Sojiro that he will become strong.

Continuing from the last episode, Sojiro thinks about his past a little bit more, and thinks of Shishio's "survival of the fittest", and Kenshin's way of not killing people. Sojiro gets very confused, not knowing which person to believe, and he suddenly breaks down during the fight. He goes crazy, and tells Kenshin that he is only getting in his way, and that the very fact that he's in the room makes him ticked off. Sojiro then fights Kenshin at his full strength, using an attack he named the Shu Ten Satsu its a combination of the shukchi speed and the Battojutsu of the tenken. Then they both do a Battojutsu stance. Kenshin emerges victorious by using his ultimate attack, the Amakakeru Ryu no Hirameki on him. Sojiro then tells Yumi to return his Wakizashi to Shishio, and also gives Yumi the details of Kenshin's ultimate attack, as a parting gift Sojiro leaves Shishio's side forever, and Kenshin and the others make their way to the final battle with Makoto Shishio.

As Kenshin, Sanosuke, and Yumi make their way to the top of the Inferno Arena, Kenshin thinks about his past, and what awaits him next, the entire way up to where Shishio himself is waiting. However, Kenshin is ready and prepared to the final battle with the manslayer known as Shishio. Upon reaching the door at the top, Yumi pulls the switch to open the door. Shishio is standing in the middle of the arena, and Houji is also there. After a few opening words with Kenshin and Shishio, Shishio promises Yumi that the battle will end quickly. He gives Yumi a kiss, walks off, and the fight between the two manslayers begins! Shishio shows off his first Secret Sword attack, the Homura Dama. He then bites a chunk off of Kenshin's shoulder.

The fight between Kenshin and Shishio continues. Kenshin and Shishio then start talking about Shishio's greatest shura that he trained himself, Sojiro. Shishio doesn't believe that Kenshin understands the laws of nature, and then he tries to show it to Kenshin, by using the Homura Dama. However, after creating a circle of flames around Kenshin, he picks him up, and ignites the gunpowder tucked inside his gauntlet. This the second Secret Sword attack, known as the Guren Kaina. This knocks out Kenshin, nearly causing his death! However, not all hope is lost. Saito busts through the door, using his Gatotsu attack (the first style). Due to a metal protection on Shishio's forehead, this doesn't affect him. After trying all of the Gatotsu styles, Saito gets knocked out by Shishio. Sanosuke attempts to attack him, but fails. Suddenly, when all hope seems lost, Aoshi appears to engage in combat with Shishio.

After a short conversation between Aoshi and Shishio, they both engage in combat with each other. However, even with Aoshi's Kaiten Kenbu Rokuren, he cannot defeat Shishio. Suddenly, after buying enough time for Kenshin, Kenshin himself appears to be standing! Due to his swordsman spirit, he was able to survive the wounds caused by the Guren Kaina. Now round two commences. Just when Shishio is about to finish Kenshin off with another Guren Kaina, he remembers the promise he made to Kaoru to go back to Tokyo together. He then uses a five-hit combo on Shishio, and does the Ku Zu Ryu Sen, of the Hiten Mitsurugi Style. Shishio gets back up because of his swordsman spirit, and the final round is about to commence.

Getting back on his feet after the Ku Zu Ryu Sen, Shishio gets ready to use the final and ultimate Secret Sword attack, the Kaguzuchi. Kenshin also prepares to use his ultimate move, the Amakakeru Ryu no Hirameki. The attacks end up cancelling each other, but the resulting vacuum, temporarily immobilizes Shishio. Not missing his chance, Kenshin strikes. Shishio miraculously stands back up, but as it has been far longer than fifteen minutes, his blood starts evaporating. In fear of Shishio's life, Yumi rushes in, and begs Kenshin to spare him. However, Shishio stabs Kenshin through Yumi! He is determined to continue fighting, and Yumi dies, knowing she did something useful for once. The battle is once again at a standstill. Then suddenly, the scorching heat in Shishio's body causes him to end up being burned alive once again, this time fatally. Houji, refusing to accept Shishio's defeat, maniacally attempts to destroy the Inferno Arena to take out Sanosuke, Kenshin, Saito, and Aoshi.

Sano and Aoshi drag an unconscious Kenshin as they run from the burning Building. They eventually escape, but Saito was left behind because his legs were too injured to jump the bridge/walkway that had collapsed. So Saito is now presumed dead. Chou the Swordhunter also appears to tell the group what was happened to the rest of the Juponggottana. The episode ends with Makoto Shishio, Yumi, and Houji gathering in hell, scheming how to take over.

Yahiko visits Mount Hiei, and Sanosuke shows him where that battle with Shishio took place. Meanwhile, Kenshin visits an unknown woman's grave, and places flowers by it. Also at this time, Megumi explains to Kaoru the severity of Kenshin's wounds, and that it is important to keep him from doing anything that dangerous again. Finally, the gang gets on the train to Tokyo, with Misao waving to them and telling them to visit again. After the train departs Saito is seen saying that he and Kenshin will meet again one day and settle the score that they have. When the gang reaches the road to the dojo, Kaoru extends her hand and welcomes Kenshin home. Kenshin smiles and says, "It's good to be home."