Story Summary
The Tokyo Arc It begins when Kenshin Himura, the legendary 'Hitokiri Battousai' meets Kaoru Kamiya and she invites him to stay at her dojo. The two then meet Yahiko Myojin, who becomes Kaoru's only kenjutsu student and second live in border after they rescue him from a local yakuza gang. Shortly after that the trio meets Sanosuke, who becomes a constant meeting at the Kamiya dojo after Kenshin turns his perspective on life around when he defeats him in a duel. This group of four gains yet another member when they rescue Megumi Takani, a hopeful doctor from the avaricious businessman Kanryu Takeda and the Oniwaban ninja group, lead by Aoshi Shinomori. Although Kenshin has settled down for the time being life is anything but peaceful.The Kyoto Arc
Unlike in the Tokyo arc it has a very strong ongoing storyline. The Kyoto arc is definitely a must see episodes.
Kenshin is very satisfied with his new life at the Kamiya dojo, but this happiness doesn't last and before long his past as the 'Hitokiri Battousai' comes back to haunt him with the return of his long-time adversary, Hajime Saitou. It turns out that a man that was thought to be lifeless is secretly making plans to take over the new Meiji government. That man turns out to be none other than Kenshin's successor from back during the Meiji Restoration, who is a heavily bandaged lunatic named Makoto Shishio. For the sake of Japan, Kenshin is forced to make an alliance with Saitou and leave the Kamiya dojo and depart for Kyoto in order to defeat Shishio. Not deficient anyone to get hurt by following him, Kenshin leaves without saying goodbye to anyone but Kaoru. However, everyone has gotten quite fond of to Kenshin and they aren't exactly agree with the idea of him leaving and possibly never coming back. Kaoru and Yahiko travel to Kyoto to look for him and so does Sanosuke. In the intervening time while traveling to Kyoto Kenshin meets Misao Makimatchi, a female ninja from the Oniwaban-shu. Misao is trying to find and reunite with Aoshi Shinomori (one of Kenshin's enemies from the Tokyo arc). Aoshi in the meantime is also back in the picture and he's willing to go to great lengths for a chance to defeat Kenshin. As the insane Shishio assembles his fighting force, Kenshin also has to make his own planning for battle, including returning to his old master, Seijuro Hiko in order to finish his trainin . Kenshin must also find a way to defeat Shishio and his band of followers while still maintaining his vow to never kill.
The Jinchuu Arc
Life seems to have settled down after the ordeal in Kyoto and Kenshin seems to have to finally settle down for good. And then suddenly a lot of people who are close to Kenshin are being attacked. It turns out that the attacks are being lead by Enishi Yukishiro. Enishi hates Kenshin with the flaming passion of a thousand suns (I just had to put that in somewhere) because he holds him responsible for the death of his sister, Tomoe. Enishi has been waiting all of this time to exact his revnge on Kenshin, along with his group of skilled fighters who each want Kenshin dead for one reason or another. Enishi wants to hurts those around Kenshin so that he will suffer as much as possible. Kenshin decides to tell the others about what happened in his past. It turns out that Kenshin was actually married to Enishi's sister Tomoe but he accidently killed her when she jumped in front of him during a battle. Enishi was present when this happened but he didn't see everything and so to him it looked as if Kenshin had killed Tomoe on purpose. With some help from Aoshi (who decides to take some time off from meditating) and Misao, the Kenshin hope to defeat Enishi and his group as well as make him see that Kenshin didn't intentionally kill Tomoe.
This arc is called the Jinchuu arc because of Enishi always refers to his mission to kill Kenshin as his 'Jinchuu' or 'divine justice'.Tsuioko Hen
The Tsuioko Hen appeared in the middle of the Jinchuu arc. The OVA follows Kenshin's life before the beginning of the Tokyo arc starting from the time he was a child and was rescued by Hiko from bandits. Shortly after parting ways Hiko over a dispute on how the Hiten Mitsurugi style should be used Kenshin joins the Choshuu Inshin Shishi as its shadow assassin. One of the men that he assassinates along the way is a man named Kyosato Akira who gives Kenshin the first half of his cross scar before dying. Not long after, Kenshin meets Tomoe, who witnesses him killing someone and then faints. Unknown to Kenshin, Tomoe was engaged to Kyosato before Kenshin killed him. He decides to take her back to his headquarters where she stays and works. Kenshin's boss Katsura tells Tomoe to become Kenshin's 'sheath' and protect him from becoming an unrepentant killer. Eventually things become very bad for the Choshuu Inshin Shishi and Kenshin and Tomoe are forced to flee Kyoto and hide in the countryside, posing as husband and wife. As time goes by Kenshin and Tomoe fall in love but things turn ugly when Kenshin's supposed friend Iizuka betrays him and turns him over to the Shogunate. It also turns out that Tomoe was also working as a spy for the Shogunate against Kenshin but now that she loves him she doesn't want him hurt.
Seisou Hen
There are only 2 episodes in this OVA.
The story mainly focuses on Kenshin and Kaoru and their history together during and after the series. Flashbacks include the most memorable moments from the different arcs as well as rather surreal dreams involving certain characters and events.The Filler Arcs
The first one is where the Kenshin has to stop a man named Shougo Amakusa who says he is the son of God from building a Christian empire in Japan. There's also a side-plot involving Shougo's younger sister Sayo, who's dying of Tuberculosis and Sanosuke who loved her tries to saves her.