The Kyōto Arc is the second arc of the Rurouni Kenshin manga. According to the dates set within, the entire arc takes place in the span of three months, beginning on May 5, 1878 and ending around the Kyōto Obon Festival, on August 15, 1878. This arc runs through one of the major repercussion's of Himura Kenshin's actions, as a major antagonist is born, due to his exploits during the Bakumatsu, the successor of Hitokiri Battōsai: Shishio Makoto.
A Familiar Face Returns
The arc begins when Kenshin is confronted by his old adversary, Saitō Hajime, who is now a Lieutenant of the police force and appears before Kenshin as an enemy once again (though in reality, he is simply commanded to test Kenshin's abilities by police commissioner, Kawaji Toshiyoshi). Okubo Toshimichi, the leading politician in Japan, appears along with Kawaji in the Kamiya Dōjō where the battle is being held and at the final moment Kawaji's voice prevents Saitō and Kenshin from killing one-another (since they are so deeply absorbed in the battle, that they are unaware of their surroundings and can only hear the voices of those, who like themselves, have witnessed the horrors of the Bakumatsu).
Kenshin is asked by Okubo to head towards Kyōto and kill Shishio Makoto, the man who took over his duties as Hitokiri, in the shadows and is now planning to create a new Japan, where only the strongest survive, with himself as its absolute overlord. After no clear decision is made, Okubo asks to meet Kenshin on the 14th May, so that he can make his final decision. Okubo is later killed by Shishio's top henchman, Seta Sōjirō, just as Kenshin goes to meet him and this prompts Kenshin to go to Kyōto and thwart the plans of Shishio. He is thus forced to say goodbye to Kamiya Kaoru and renew his journey as a Rurouni. After moping and not eating for a few days, Kaoru is harshly reprimanded by Takani Megumi and Myōjin Yahiko influences her to travel to Kyōto along with him in the hopes of finding Kenshin and bringing him back to Tokyo.
Sagara Sanosuke, likewise heads towards Kyōto, although Saitō confronts him just as he is about to leave telling him that he is a weakness for Kenshin and that if he goes to Kyōto he'll only get in the way, because he is not strong enough to be battling Shishio and his henchmen. This infuriates Sano, who tries to attack Saitō, but is once again beaten up by him, even when Saitō plays Sano's game and fights in hand-to-hand combat, putting his sword aside. Sano still refuses to give up, saying that Saitō's attacks don't hurt nearly as much as him being treated by Kenshin as his weakness and so Saitō let's him that he can do whatever he wants and heads off. On his way to Kyōto, Sano keeps getting himself lost in the middle of nowhere, until he meets Yukyuzan Anji, a fallen Buddhist monk. Upon seeing Anji using turning figures of solid stone into dust, by slamming his short sword into the ground, Sano asks that he train him, to which Anji eventually agrees. During the training he is visited by the spirit of his former mentor, the deceased Sagara Sōzō, and by the end of one week, he masters the technique of Futae no Kiwami, with his right hand, which deeply impresses Anji.
On the way to Kyōto, Kenshin meets a young tomboyish girl named Makimachi Misao and is surprised by her combative skills. He later learns that she is a member of the Oniwabanshū Ninja clan, who is searching for Shinomori Aoshi, the clan's leader and Kenshin's former adversary, whom he defeated in a hard-fought battle in Tokyo a while ago and his 4 students (Beshimi, Hyottoko, Shikijō and Han'nya). Kenshin hides the truth from Misao, knowing that news of the deaths of Aoshi's students (her former comrades, whom she looked up to as a child), would wound her deeply. They later head to Shingetsu village, controlled by Shishio, where Kenshin meets Saitō once again. Learning that Shishio is in the village at this time, Kenshin and Saitō pay Shishio a visit and are followed by Misao and a young orphan boy whom Kenshin rescued, named Mishima Eiji, who's family are the victims of a powerful henchman of Shishio, named Senkaku. Upon seeing that his predecessor is a Rurouni and no longer a Hitokiri, Shishio is dissappointed and first has Senkaku battle him and after Senkaku loses, he leaves his fate up to Sojiro, whom Kenshin battles to a stale mate (although the battle results in Kenshin's Sakabatō being broken). Saitō adopts Eiji and sends him away to his wife Tokio, while Kenshin and Misao head towards Kyōto.
When in Kyōto, Kenshin meets Misao's caretaker, Kashiwazaki Nenji of the Aoiya (aka Okina), the truth about Aoshi and the others and knowing that Kenshin's cause is righteous, Okina seeks to aid his efforts, helping him find a sword smith (Arai Seikū) who can create for him, a new Sakabato and later, his old master, Hiko Seijūrō, whom he wishes to meet in order to master Hiten Mitsurugi-ryū completely so that he is strong enough to face Sojiro and Shishio. Seiku initially asks that Kenshin excuse him from making a sword, since he has abandoned his father's (Arai Shakku) tradition of making weapons of murder, but after his son Iori is kidnapped by one of Shishio top henchmen, Sawagejō Chō, Seiku gives Kenshin his father's final sword (white later turns out to be a Sakabato), whereby he easily defeats Cho, despite earlier setbacks as a result of having to fight with a broken sword. Kenshin thus leaves the Aoiya, much to Misao's dissappointment. When chasing after Kenshin, she unintentionally misses Aoshi who happens to be crossing by in the opposite direction and at the same time Kaoru and Yahiko, who are now in Kyōto, chase after Aoshi and unintentionally miss Kenshin. Misao bumps into Yahiko and she later learns that Kaoru and Yahiko are chasing after Kenshin. She then takes them to the Aoiya and Okina reluctantly tells them of Kenshin's whereabouts, whereby all three of them head to meet him.
Meanwhile, Aoshi is hunting Kenshin, under the pretext that if he defeats him, he will earn the title of 'strongest', which he can adorn upon the graves of his fallen students. He thus forms an alliance with Shishio, who offers to provide him information on Kenshin's whereabouts, in return for Aoshi simply killing the latter.
Reunion with the Old Master
Kenshin meets his old master for the first time in 14 years, though Hiko is extremely displeased at him for having left him in the first place. He refuses Kenshin's request to learn the final techniques of Hiten Mitsurugi-ryū. As he walks away, Kenshin grabs his leg and begs him to teach him. Hiko says that he is an idiot whom he should never have taught him in the first place. Yahiko and Misao overhear this (as the two of them along with Kaoru are now at Hiko's residence) and barge in angrily. Hiko realizes that they are Kenshin's friends and is surprised at the popularity of his "idiot apprentice". He then asks Kenshin to go get water, while he speaks with his friends, in order to learn what he's been up to from their perspective, rather than his. Knowing that Kenshin has finally adopted the true meaning of Hiten Mitsurugi-ryū, i.e. to protect the people from the pains of the times, but not to be affiliated with any form of political power and thus agrees to teach him Hiten Mitsurugi-ryū's ultimate techniques (Kuzuryūsen and Amakakeru Ryū no Hirameki), which he eventually learns with great difficulty.
Shishio's spies infiltrate the Aoiya in hopes of capturing Okina, whom they desire to interogate for Kenshin's whereabouts, but are easily defeated by the skilled Ninjas of the Oniwabanshū. Okina now knows of Aoshi's treachery and sends him a secret message, desiring to meet and challenge his old comrade. When the two battle, Okina learns that Aoshi's far surpassed his previous limits and even the old Okashira (leader) of the Oniwabanshū, but still continues fighting. He is eventually hacked up and left fatally wounded near death by Aoshi, just as Misao walks in and sees what has occurred. Misao is heart-broken at what Aoshi has done and after Okina is brought to the Aoiya to be taken care of, Misao is shown Okina's final will and testament by some of her comrades of the Oniwabanshū. In it, he asks Misao to stay away from harm and leave the battle with Shishio to Kenshin, but Misao is determined to help Kenshin defeat Shishio and Aoshi both and declares herself the new Okashira of the Oniwabanshū.
Sano in Kyōto
Sano is currently in a Kyōto prison, having purposefully gotten involved in a scuffle with some police officers, in order to find any way to get in touch with Saitō, who could lead him to Kenshin one way or another. Saitō eventually finds him, but pretends not to know who he is, simply walking away. Sano then breaks through his prison cell using his newly learned Futae no Kiwami. Saitō realizes that Sano took has gotten stronger, but asks him if he's worked on defensive techniques as he had advised him to do. Sano then crudely tells him that he has his own method of fighting that doesn't involve defense. Cho is currently in prison and Saitō and Sano go inside to question him, regarding the identify of a dangerous killer, who was able to murder 50 skilled police officers in the space of one hour. Cho tells him that only two members of the Juppongatana would have been able to do as such, namely Seta Sōjirō and Uonuma Usui. Cho tells Saitō that even though the latter's is highly skilled, he would be no match for Usui and Saitō expresses his interest at the prospect of fighting an opponent like him. Cho also tells Saitō about Shishio's plans to burn down Kyōto in order to take advantage of the chaotic situation and expand his power.
After mastering Hiten Mitsurugi-ryū's final techniques, Kenshin goes off to meet Saitō, but as soon as he enters the room that Saitō's in (in the Police Headquarters), he is punched in the face by Sano and after a short while collapses in his arms, as a result of the hard blow. Sano tells him that he should never have wandered away without informing him first and Kenshin simply smiles. Kenshin, Saitō and Sano then try to work out Shishio's plans, so that they can act to thwart them. Kenshin realizes that Shishio's real plan is to attack Tokyo directly and that the Kyōto fire is simply a diversion. He sends Misao and Okina a letter, informing them of the situation and telling them to be prepared to prevent the fires.
Battle on the Rengoku
Kenshin and Saitō attack Shishio's forces on the Rengoku ship, while Sano destroys the ship's interior from the outside, as per Kenshin's request, using bombs given to him by his good friend Tsukioka Katsuhiro while about to leave Tokyo for Kyōto. Shishio is surprised by the trio's successful endeavor and leaves them with a message: that they are to meet him and his henchmen for a final showdown in his temple several days later (although Sano is outside the ship at this time). Kenshin agrees, knowing that a showdown on the ship will injure too many bystanders, while Saitō questions the former's decision.