Tajemniczy wojownik zjawia się w japońskiej szkole sztuk walki w okresie Meiji, przypadkowo znajdując się w samym centrum konfliktu na tle handlu opium.
Back at home, Kaoru works to restore the dilapidated dojo, while Kenshin encounters a wise old fisherman who teaches him an important lesson about love.
Sanosuke adopts a stray dog, unaware that it holds the key to a criminal gang's plot to blackmail some local officials and gain political control. And when the gang finally tracks him down, Kenshin and Yahiko join Sanosuke to foil their plan.
After Kenshin finds a ring inside a catfish, he's persuaded to give it to Kaoru. Thinking it's an engagement ring, Kaoru is sure that he's asking her to get married.
Alerted by Misao, Kenshin and the rest of the Peace Force arrive to help Aoshi find a mysterious killer. Kenshin's investigation uncovers evidence linking the killing to a Christian swordsman and of vengeance that's been foretold.
As Kenshin prepares to honor his promise to stop Shogo Amakusa, he and Sanosuke uncover a secret church that was built when Christian worshipers were forced underground.
When neither Kaoru nor Kenshin can persuade Shogo Amakusa to abandon his plan to advance the Christian cause through violence, the stage for battle is set.
As Kenshin tries to stop the slaughter of the Christians as they march towards martyrdom, Sanosuke is unable to avert the death of Shogo's terminally ill sister.
When the Peace Force comes across a man posing as Kenshin, everyone else wants the impostor exposed. But Kenshin notes that he's been using his profits to care for a group of orphans.
After their search leads them to the hidden cure, the leader of the Black Knights makes it clear that he has no intention of honoring his promise to cede control of Japan to the Sanada Ninjas.
As Aoshi arrives to bring her home, Misao joins Kaoru and some friends for a final shopping spree. However, Sanosuke and Yahiko's efforts to keep an eye on the women lead to them to be mistaken for a pair of thieves.
Following a series of accidents in town, a master of feng shui blames an imbalance in the Ki, a force which keeps all of nature's other forces in balance.
As Kenshin learns of a battle between the Wind and Water families for control of the Ki, efforts to build a railroad are exposed as a Water clan plot to control Japan.
With help from the Wind family's leader, Kenshin saves Kaoru's life. But the Water family's quest to redirect the Ki and gain control of Japan moves ahead as planned.