The Meiji Era was one of great renewal for Japan, where swords and killing were outlawed. However, many survivors from the time of Revolution still live, lurking in the shadows and waiting for a chance to use their killing blades again. Only Kenshin Himura, formerly one of the most brutal of killers, hopes to keep his swordsman's honor and still live in the new era.
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.
After stepping in to stop what appears to be a robbery, Kenshin and Kaoru meet a young prince who looks exactly like Yahiko.
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 Samurai and of vengeance that's been foretold.
In an effort to prevent more revenge killings, Kenshin must take on Shogo Amakusa, the Christian warrior known as God's Child.
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.
Though blinded by his duel with Shogo Amakusa, Kenshin seeks another battle in hopes it will restore his sight.
Along with the story of his parent's martyrdom, Misao uncovers the truth behind the alleged miracles that deified Shogo Amarusa.
Sir Kaioh unveils his plan to use Shogo Amarusa's loyal followers to overthrow the government and control Japan himself.
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.
As Misao and the Dutch consul ask the Army delay to their attack, the sightless Kenshin pressures Shogo to prevent the martyrdom of his followers.
Following Shogo's surrender, Kenshin asks the government not to execute him. As a result, he and his followers are sent into exile in Holland.
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.
When Kenshin accidentally loses all their money, the Peace Force must go to work at an inn in order to pay their bill.
Kaoru offers to take on a scholarly young student who's been expelled by his teacher until he learns how to fight.
As Kaoru continues her training of Daigoro, Kenshin is warned to steer clear of the young man's teacher, Kaishu Katsu.
Despite Kaishu's determination to free his daughter on his own, Kenshin joins the Peace Force and Daigoro for a rescue.
Though Daigoro is wounded in the battle, Kenshin and company free Itsuko.
With his arm nearly healed, Yutaro and his doctor arrive for a visit at the dojo.
When a letter from Dr. Hans reveals the story of the miraculous medicine, Yutaro joins the Peace Force in an effort to find it.
Using the clues left behind by Dr. Hans, Kenshin and company are led to the hidden shrine that holds the key to the miracle cure.
After surviving a fall into a volcano, the Peace Force comes across an injured Sanada Ninja who offers to help battle his former allies.
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 he faces off against the Black Knight's leader, Kenshin must rely on his brains and not his sword to win the battle.
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.
The Water family's efforts to gain control of the Ki have left Kaoru seriously wounded.
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.
With Kenshin's help, the Wind family derails their rival's plan to redirect the flow of the Ki and ends their effort to dominate Japan.