After participating in the Boshin War as the assassin Hitokiri Battōsai, Himura Kenshin wanders the countryside of Japan, offering protection and aid to those in need as atonement for the murders he once committed.

After discovering that Kenshin is the true Hitokiri Battōsai, Kaoru offers him a place to stay at her dojo, noting that he is peace-loving and not cold-hearted, as his reputation had implied.

Kenshin accepts and begins to form lifelong relationships with others, including Sagara Sanosuke, a former member of the Sekihō Army; Myōjin Yahiko, an orphan from a samurai family who also lives with Kaoru as her student; and doctor Takani Megumi, who has become involved in the opium trade.

After his first meeting with him, Kenshin realizes that he must become stronger to defeat Shishio without becoming the cold assassin he was in the past and returns to the man who taught him kenjutsu, Hiko Seijūrō, to learn the school's final technique.

Finally accepting the help of his friends, he defeats Shishio, who dies after exceeding the limits of his abnormal body condition, after which a reformed Shinomori stays in Kyoto with the surviving Oniwabanshū.

[3][4] The first story, published in December 1992 in the Weekly Shōnen Jump Winter Special issue of 1993, featured an earlier version of Kenshin stopping a crime lord from taking over the Kamiya family dojo.

[3] The second Rurouni story, published in April 1993 in the Weekly Shōnen Jump 21–22 double issue of that year, featured Kenshin helping a wealthy girl named Raikōji Chizuru.

In contrast to the YuYu Hakusho young lead Yusuke Urameshi, Kenshin was written as an adult with a dark past based on the Edo period in order to make the series stand out.

Kenshin's age was also a departure from common archetypes in manga as the themes and lore in the story made him an adult in contrast to other young protagonist besides City Hunter.

However, he tried writing a realistic series and avoid supernatural powers regardless of the young demography with few exceptions being Yukishiro Enishi's ability to perform double jumps to counterattack Kenshin's aerial style.

[11] For its seventh volume, Watsuki's boss suggested to him that it was time to make a longer story arc, which resulted in the creation of the fights between Kenshin and Shishio Makoto.

[16] The story took on a darker tone as most of the characters believed Kaoru was killed by Yukishiro Enishi, which made Kenshin question his own way of living and escape to a village of wanderers.

[11] Even though the plot for the "remembrance episodes" of Kenshin's past was already set before serialization started, which was three and a half years before her debut, Watsuki was filled with regrets about how he portrayed Yukishiro Tomoe for unspecified reasons.

[27] Marco Olivier from the Nelson Mandela Metropolitan University said that the sakabatō symbolizes Kenshin's oath not to kill again, which has been found challenging by other warriors appearing in the series.

[33] Since the manga focuses on realism but is aimed at young readers, the series is notable for changing the portrayals of samurais in order to create a more optimistic take in comparison to real-life events.

[49] In 2014, Watsuki wrote a two-chapter spin-off titled Rurouni Kenshin: Master of Flame for Jump SQ., which tells how Shishio met Yumi and formed the Juppongatana.

[50][51][52] Watsuki and his wife, Kaworu Kurosaki, collaborated on a two-chapter spin-off titled Rurouni Kenshin Side Story: The Ex-Con Ashitaro for the ninth anniversary of Jump SQ.

In 2021, Watsuki created the manga "Sakabatō Shogeki" (逆刃刀 初撃, "Reverse-Blade Katana: First Bout") that was exclusively shown at an exhibition celebrating the 25th anniversary of Rurouni Kenshin.

[103] The second one, Rurouni Kenshin: Meiji Kenkaku Romantan: Jūyūshi Inbō Hen (るろうに剣心 -明治剣客浪漫譚- 十勇士陰謀編 - The Ten Warrior Conspiracy), was released on December 18, 1997, and was re-released in the PlayStation The Best lineup on November 5, 1998.

[116] Rurouni Kenshin has been highly popular, having sold over 55 million copies in Japan alone up until February 2012, making it one of Shueisha's top ten best-selling manga series.

[125] In November 2014, readers of Da Vinci magazine voted Rurouni Kenshin as the thirteenth Weekly Shōnen Jump's greatest manga series of all time.

[132] Watsuki's writing involving romance and Kenshin's psychological hidden weakpoints also earned positive responses from other sites, with AnimeNation also comparing it to Clamp's X based on the multiple elements of the series.

[135] As a result of the series taking a darker tone in later story arcs with Kenshin facing new threats and at the same time his Battosai self, Kat Kan from Voice of Youth Advocates recommended it to older teens.

[136] This is mostly noted in the "Kyoto arc", where Mania Entertainment writer Megan Lavey applauded the fight between Himura Kenshin and anti-hero Saito Hajime, which acts as the prologue of such a narrative.

[138] The eventual climax led to further praise based on how menacing Shishio is shown in the battle against his predecessor, although he questioned if Kenshin had been a superior enemy if he had kept back his original killer persona.

Zac Bertschy from Anime News Network (ANN) praised the story from the manga but noted that by volume 18 of the series, Watsuki started to repeat the same type of villains who were united to kill Kenshin, similar to Trigun.

[144] While also liking their final showdown, Megan Lavey from Mania Entertainment felt that the twist that happens shortly after the battle is over serves to show Enishi's long-life trauma and, at the same time, Kenshin's compassion towards others.

[135] In Bringing Forth a World: Engaged Pedagogy in the Japanese University's seventh chapter, "The Renegotiation of Modernity", by media studies professor Maria Grajdian, Kenshin's heroic nature as a wanderer was compared to both Luke Skywalker and Harry Potter due to how he wishes to protect the weak people, seeing nothing wrong with such trait.

In doing so, Rurouni Kenshin laid" more than twenty years ago the foundation of a fresh paradigm of humanity based on tenderness and mutual acceptance as a counter-movement to the individualism, competition and efficiency that characterize the project of modernity".

[148] For the series 25th anniversary in January 2021, 15 manga authors sent congratulatory messages: three of Watsuki's former assistants, Eiichiro Oda (One Piece), Hiroyuki Takei (Shaman King), and Shinya Suzuki (Mr. Fullswing); Nobuyuki Anzai (Flame of Recca); Riichiro Inagaki (Eyeshield 21); Takeshi Obata (Death Note); Masashi Kishimoto (Naruto); Mitsutoshi Shimabukuro (Toriko); Hideaki Sorachi (Gintama); Yasuhiro Nightow (Trigun); Kazuhiro Fujita (Ushio & Tora); Yusei Matsui (Assassination Classroom); and Kentaro Yabuki (Black Cat).