The Kenshin-gumi's brief period of peace is interrupted by the presence of former Shinsengumi captain Saito Hajime - now using the name of Fujita Goro and working for the Tokyo police - stirs up some of Kenshin's bloodiest memories of the Bakumatsu. Saito arrives at the Kamiya dojo disguised as a medicine seller and fights Sanosuke, injuring him severely in the process.
Sanosuke is beginning to recover from the wounds inflicted by Saito, but Kenshin's mind is greatly disturbed. Akamatsu, another assassin hired by the same man who is paying Saito fights Kenshin by drawing him out but loses to Kenshin while Saito arrives at the dojo using his status as a policeman to gain entrance. Kenshin and Saito begin to fight, despite Kaoru's attempt to stop them as she begs Kenshin not to revert to his Battousai persona.
The battle between Kenshin and Saito continues after Kenshin is stabbed by Saito's Gatotsu Sanshiki. Kaoru is frightened to see Kenshin's Battousai persona begin to emerge and begins to lose hope that she will ever see the gentle Rurouni again. However, one of Saito's superiors appears and stops the fight just as it is reaching a climax and Kenshin returns to normal after punching himself in the face. Okubo explains to Kenshin that Shishio Makoto, the man who took over Kenshin's position as the Shadow Hitokiri for the Ishinshishi survived being burned alive and has begun gathering an army to overthrow the government, and hopes that Kenshin can defeat him, with the threat of Megumi being turned in for opium manufacture unless he complies. Megumi states she would rather die that be used as a pawn against Kenshin, and he is given a deadline upon which to decide.
As the deadline for Kenshin's decision on whether to go to Kyoto nears Kaoru becomes anxious at the possibility of his leaving. After Okubo's assassination by Seta Sojiro, Kenshin decides to go to Kyoto and bids an emotional goodbye to Kaoru, implying that it is likely they will never meet again.
Kaoru is deeply depressed and distressed since Kenshin left Tokyo. With the help of Tae, Yahiko, Tsubame, and especially Megumi, Kaoru regains her courage and decides to leave Tokyo to go to Kyoto and see Kenshin. Saito also gets into a fight with Sanosuke, telling him not to go to Kyoto. Sanosuke leaves on his own despite Saito's warning that he will be a liability to Kenshin.
Aoshi Shinomori has now chosen the path of chaos. He will do anything to defeat Kenshin, as he feels it will prove to the world that the Oniwaban Group were the strongest fighters of the Revolution. Aoshi defeats four monks working for Shishio, who were merely meant to test Aoshi's strength, but refuses to join Shishio after Sojiro tries to convince him.
Makimachi Misao, the girl bandit, whom Kenshin meets in the forest, is a member of the Oniwaban Group. She wants very badly to see Aoshi and the other four Oniwaban Group members, though she is unaware of the fate of the four Oniwaban ninjas, and she doesn't yet know the whereabouts of Aoshi. Misao refuses to stop chasing Kenshin, as she believes that he can lead her to them.
Along the way to Kyoto, Kenshin and Misao come across a nearly dead man with his little brother in his arms, Eiji Mishima. The man dies, and Eiji wants to avenge his brother's death by killing Senkaku, the man who slayed his elder brother. Kenshin, Eiji, and Misao travel to Shingetsu Village, Eiji's hometown, and fight some of Shishio's soldiers off. Saito and Kenshin leave Misao and Eiji behind, as they go to Shishio's mansion nearby.
Kenshin and Senkaku fight, and Kenshin wins with ease. Misao and Eiji make their way up to the same mansion in an attempt to defeat Senkaku for themselves.
Shishio is then challenged by Kenshin, but Shishio refuses to accept, saying that Kenshin is weak as a wanderer, and that even if there were 100 of him, Kenshin could not defeat Shishio as Kenshin is now. Shishio tells Sojiro, his right hand man, to fight Kenshin instead. Shishio and Yumi leave the mansion. Sojiro and Kenshin both use the battojutsu drawing technique. Kenshin's sword is broken in two, and Shishio's Nagasoni Kotetsu, which he gave to Sojiro to fight Kenshin with, is also severely damaged. Sojiro leaves the mansion, telling Kenshin to get a new sword before they meet again.
Sanosuke gets lost in a forest. He finds a monk there that goes by the name of Anji. Anji gives Sanosuke some food. Sanosuke ends up convincing Anji to teach him how to use the Futae no Kiwami, a very destructive punch (so destructive that it can completely pulverize huge boulders into dust with a single punch). Sanosuke has one week to learn it or Anji will kill him. Sanosuke finally learns it, and then leaves for Kyoto.
Kenshin and Misao make it to Kyoto. There, they meet Okina and four other members of the Oniwaban Group. Okina knows Kenshin is the legendary Battousai the Manslayer the moment he lays eyes on him. Kenshin goes to see Sekku Arai, Shakku Arai's son (Shakku was the one who made Kenshin's Reverse Blade Sword that broke) to get a new Reverse Blade Sword. Sekku refuses, saying that this is a time of peace, and that the samurai have all thrown their swords away. Later, Chou the Swordhunter of the Jupongottana abducts Iori, Sekku's baby son. Kenshin demands that Chou release Iori.
Kenshin finds Sawagejo Cho has kidnapped the child of Shakku's son in order to obtain Shakku's final work for himself. Kenshin is forced to choose between keeping his vow not to kill and saving the baby, deciding to save the child and draw the sword he has been given. However, just when it seems he has broken his vow and killed Cho, it is revealed that the sword he is holding is Shakku's final work, Shinuchi, a sakabato, and Cho is merely stunned. Kenshin then leaves to find his master, Hiko Seijuro, in order to learn the final technique of Hiten Misturugi-Ryu.
Kenshin finds his master Hiko Seijuro living as a potter near Kyoto, but Hiko is initially unwilling to take Kenshin back due to his walking out to join the Revolution. Yahiko and Kaoru meet Misao in Kyoto after learning that she saw Kenshin leaving, and later leads the grateful pair to him after they meet Okina at the Aoi-Ya. Kenshin seems initially upset at the sight of Kaoru, but later replies he is only "half" angry. They leave Kenshin to train, and on the way Misao's affiliation with the Oniwabanshu is revealed as well as the fact that she does not know of the fate of Aoshi's group in Edo.
Misao is in denial after hearing of the deaths of Aoshi's men, and feels despair as she recalls her country-wide search for Aoshi, which ended without success. Meanwhile, Aoshi sends a letter to Okina and they meet in a Kyoto market, where Okina tells Aoshi that his desire to kill Kenshin has turned him into a demon, and that as the leader of the Oniwabanshu Okina cannot allow this to continue. Seta Sojiro and several other Juppongatana meet Aoshi and convince him to join them, as they share the goal of destroying Kenshin. After Okina mysteriously leaves with his shinobi uniform Misao realizes that the two will have a confrontation at the temple and runs to stop it, but proves to be too late as Okina falls to Aoshi's Kaiten Kenbu Rokuren, and is told by Aoshi that the next time they meet he will kill her.
The episode starts off with Seijuro Hiko remembering the past about when he first met Kenshin and while they were continuing the training Kenshin finally proves himself worthy of learning the final technique, so Hiko begins to start by teaching him the Kuzu-ryusen, a technique where it will hit 9 targets of martial arts at one time. Then Hiko instructs Kenshin to try the attack. Kenshin uses the attack flawlessly but Hiko performed one of his own and the end result is that Kenshin lost this skirmish due to his lacking in weight and size. Then after learning this Hiko proclaims "you must defeat this technique with the ultimate attack". After much worry about his friends Kenshin finally looks within himself for what he was missing in life and learns the ultimate technique, the Amakakeru Ryu No Hirameki, which is the will to live, said to be "stronger than anything". Though he has to pay a very high price.
The Juppongottana have gathered in the temple of Shishio in Kyoto, and are ready to commence the Kyoto Grand Fire and be on their path to victory.
Sanosuke, Saito, and Kenshin go to Osaka to find Shishio and his men onboard a ship. They find Shishio, and Shishio launches the Purgatory, a steel-plated battleship he paid a fortune to get. Shishio plans to use the Purgatory to launch an assault on Tokyo.
Sanosuke uses the Futae no Kiwami Anji taught him to stop Gatling gun bullets from hitting him. He then throws the bombs Katsu gave him before he left Tokyo right onto the Purgatory, damaging the engine and leaving a hole in the ship. The Purgatory eventually sinks, but not until Saito, Kenshin, and Sanosuke get off safely. Shishio issues a challenge; Kenshin can only meet him at his base and get to him by completing one-on-one fights. Kyoto is spared from the Kyoto Grand Fire as well, thanks to intervention by the Oniwaban, now headed by Misao.
Sanosuke, Saito, and Kenshin journey to Mount Hiei at the Shrine of the Six Arches to settle the score with Shishio. The first challenger of the Juppongottana in the shrine is Anji the Destroyer, the man who taught Sanosuke the basics of the Futae no Kiwami. Anji and Sanosuke duel, and Sanosuke uses a Futae no Kiwami attack at full power, called the Kiwami Hazuchi, and knocks Anji down. Sanosuke thinks he is dead, until he gets back up more angry than ever.
Anji and Sanosuke continue their duel, and Anji is reborn to salvation after talking about his past and being convinced by Sanosuke and the memories from the people of his past that he was doing the wrong thing all these years by being a destroyer. Kenshin and Saito continue on ahead to fight Usui, the second challenger of the Jupongottana.
Uonuma Usui confronts Saito while the others continue on through Shishio's mansion. Usui's claim to "True Vision" is put to the test by Saito, who sees it for what it really is - simply super enhanced hearing adopted by Usui to make up for his lack of sight. Saito realizes that Usui is in fact weak since his desire for revenge against Shishio has driven him to become a mere pawn in Shishio's game. An enraged Usui wounds Saito using the timbe, a tortoise-shell shield and blocks his vision, however, Usui is no match for Saito's Zeroshiki, a move Saito had been saving for a fight against Kenshin.
Kenshin senses something coming from Houji's room, and then senses that it is Aoshi Shinomori. He enters the room, and is determined to keep his promise to Aoshi Shinomori, and to Misao Makimachi by fighting, and bringing back Aoshi to Aoiya. Upon entering the room, Aoshi greets him, and he says that he has thrown everything away, including his four comrades, just for the moment of the duel with him and Kenshin. Aoshi is determined to win the fight and kill the Battousai, to claim the title of the strongest.
As the duel between Aoshi and Kenshin continues, Kenshin is being attacked by Aoshi while he tries to say words to Aoshi to try and wake him up; to make him become the man he used to be. Kenshin is determined to return Aoshi to what he used to be: a man of caring, and happiness, so that he can bring back the true Aoshi to Misao, and keep both promises he made to both of them. Aoshi realizes that what he has been doing was wrong all along, and they both used their final attacks on each other. Ultimately Kenshin emerged victorious and Kenshin, Sanosuke Sagara and Yumi Komagota move on to the next battle.
The battle at the Aoiya continues, as Iwanbo, Henya, and Kamatari fight against the Oniwaban Group and Yahiko and Kaoru. Yahiko manages to defeat Henya, after being almost killed by his Hikku Happa attack. After that, Kamatari, Kaoru, and Misao fight. Misao gets crushed ribs in the fight against Kamatari, and is unable to continue until she wakes up from a dream of Hannya, and she and Kaoru defeat Kamatari through a combined effort. It seems like they have won, until two other Juppongatana members, Fuji and Saitsuchi, appear. Things are not looking good for the ones who remained at the Aoiya.
Just when all hope seems lost, Seijuro Hiko shows up and fights Fuji. He talks to Fuji and makes he realize that he was being used and ask for a fair fight. He defeats Fuji with the Kuzu Ryu Sen. The Aoiya is safe from harm, but Kenshin still has to fight Sojiro in order to fight Shishio himself.
Sojiro and Kenshin have their second duel, since the one in Shingetsu Village was never finished. Sojiro shows Kenshin the Shukuchi attack, an attack that brings him to his opponent in an instant, because he uses powerful legwork. Kenshin manages to get himself pretty wounded in the fight, and Sojiro hasn't even gotten hit once. He even dodges the Kuzu Ryu Sen, an attack Hiko said was unblockable.
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 blades end up hitting each other and the attack does not connect properly. However, Kenshin's attack created a vacuum utilizing the Amakakeru Ryu no Hirameki and the Kaguzuchi's sheer power, and temporariliy immobilized Shishio. Not missing this chance, Kenshin strikes Shishio with an immensely strong consecutive hit. Shishio miraculously stands back up, but since he has fought far longer than fifteen minutes, his blood starts evaporating and he begins screaming in pain. In utter fear of Shishio's death, Yumi rushes over by Shishio, and begs Kenshin not to finish him off. However, Shishio stabs Kenshin through Yumi! He is determined to continue fighting, and Yumi dies happily, knowing she did something useful for once. As the battle continues, 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."