Tokyo Arc (Introduction) - eps. 1 - 27

The main characters (Kenshin, Kaoru, Yahiko and Sanosuke) are introduced, and initial conflicts arise. Here we also meet Jin-e Udou, Takani Megumi, Shinomori Aoshi and Oniwabanshuu, Yutarou and Raijuuta, Tsunan (Katsuhiro).
Filler episodes:
- 13, 14 (mostly filler), 15, 16, 17, 18
- 25 up to 27 (Pirates Arc)


Kyoto Arc - eps. 28 - 62

Saitou Hajime appears, which represents so far the major bridge to the past of Kenshin. The rurouni leaves Tokyo and Kamiya dojo and goes to Kyoto, to face Shishio Makoto and Juppongatana, who threaten the integrity and stability of the new Meiji Era. Filler episodes - eps. 63 to 66, 77 and 78, 89 - with short stories, usually showing the daily life in the Kamiya Dojo, do not influence the plot at all.



Christians Arc - eps. 67 - 76

The friends from Kyoto, the Oniwabanshuu, report strange events. Kenshin and the gang discover that there is a christian, Shougo Amakusa, who also knows the Hiten Mitsurugi style and is willing to overthrow the Government and create "paradise on earth" in Japan, in revenge for the massacres of christians in the past.




Kaishuu Katsu Arc - eps. 79 - 82 
 
Kaishuu Katsu is a former strategist who served the Shogun. An incident leads his younger student to learn how to fight with Kaoru, and Kenshin ends up trying to protect Kaishuu and his daughter from a group planning revenge against this "shogun traitor."

Commonly confusing by filler, this arc is an adaptation of one of the light novel volumes.


Black Knights Arc - eps. 83 a 88

The Black Knights are a German Freemasonry group who came to Japan pursuing a doctor who has the formula for a remedy able to cure numerous diseases, as they intend to use it as a way to manipulate and dominate the world.This doctor is also tutor to Yutarou, presented in the Tokyo Arc (along with Raijuuta). Kenshin and company have to prevent the Black Knigths and the ninja Misanagi from reaching the main element from the formula before it's too late.


Feng Shui Arc - eps. 90 a 94 

The Water and Wind families contend for a hegemony in the Ki plane for centuries. The conflict seemed to be over, but he was only asleep. Kenshin and the last member of one of these families need to prevent the city of Tokyo from being destroyed as the scene of this dispute.





Summer Special - eps. 95

The true final episode of the animated series, it was only aired in Japan. When the series was exported, the last chapter was discarded because in the West was considered unnecessary for the understanding of the series. With this, the anime seems to end abruptly with the last episode of the Feng Shui arc. This episode shows the fate of the Kamiya Dojo and implied that Kenshin and Kaoru would have stayed together in the end.



Jinchuu Arc - "Exclusive to manga"

This Arc takes place after the fight with Shishio and is exclusive to the manga. Here are shown the answers about Kenshin's past, the origin of his scar and what led him to abandon the path of the manslayer. Enemies even closely linked to his past reappear. Although not animated in series, there is a not very faithful adaptation in 6 OVA's (Tsuioku-hen and Seisou-hen).




Hokkaido Arc - Exclusive to manga (on going)

For many years, it was only an idea, but in 2016 Watsuki resumed the story with Rurouni Kenshin Ibun: Ashitarou Zenka-ari which is a prelude to this arc. It takes place 5 years after the classic series, 6 months after the special "Yahiko no Sakabatou". In addition to introducing new characters, it is known that the main idea was to bring familiar faces back to the stage as another survivors of Shinsengumi, Fuji and other former members of the Juppongatana.