In the year 1876, Japan is undergoing a major transformation under the Meiji Restoration. The feudal system is abolished, and the samurai class is losing its power and privileges. Many samurai resist the changes and rebel against the new government, while others adapt and join the modern army.
One of these samurai is Kenshin Himura, a former assassin who has sworn never to kill again. He wanders the country as a rurouni (wanderer), helping those in need with his reverse-blade sword. He arrives in Tokyo, where he meets Kaoru Kamiya, a young woman who runs a dojo that teaches kendo (swordsmanship). She mistakes him for a murderer who has been using her dojo's name to commit crimes, but soon realizes her error and invites him to stay at her dojo.
Kenshin's peaceful life is interrupted by the appearance of various enemies from his past, who seek revenge or challenge him to a duel. He also encounters new allies, such as Sanosuke Sagara, a former fighter for the anti-government forces; Yahiko Myojin, an orphan boy who wants to learn kendo from Kenshin; and Megumi Takani, a female doctor who was forced to make opium for a crime syndicate. Together, they face various threats that test their skills and ideals.
The main antagonist of the story is Makoto Shishio, a former assassin who was betrayed and burned alive by the government. He survived and formed an army of rebels who plan to overthrow the Meiji government and create a new era of chaos. He considers Kenshin his rival and wants to defeat him in a final battle.
The story follows Kenshin's journey as he struggles to uphold his vow of not killing, while protecting his friends and the people he cares about. He also learns more about his past and his role in the turbulent history of Japan. He faces many moral dilemmas and conflicts that challenge his beliefs and values. He ultimately decides to fight for the future of Japan, not for himself or for revenge.
The story ends with Kenshin defeating Shishio in a climactic battle at his fortress. He then returns to Tokyo with his friends and lives happily with Kaoru at her dojo. He finally finds peace and redemption after his years of bloodshed.