As the imperialist forces celebrate their hard-fought victory in the Battle of Toba–Fushimi, a figure known as the Hitokiri Battōsai quietly slips away from the chaos of battle, leaving behind his sword, which is subsequently claimed by the fallen Udō Jin-e. Fast forward a decade, Saitō Hajime and his police comrades are embroiled in the investigation of an undercover officer's murder, which they suspect might be the work of the infamous Battōsai. However, Saitō holds his suspicions for Takeda Kanryū, a wealthy yet malignant businessman.
Meanwhile, the former Battōsai now goes by the name Himura Kenshin, and he arrives in Tokyo. While exploring the city, he encounters Kaoru Kamiya, the proprietor of a Kendo school that once belonged to her late father. Her dojo’s reputation has been tarnished by someone falsely claiming to be the Battōsai, leading Kaoru to mistakenly confront Kenshin, believing him to be the notorious assassin. The encounter is tense, but Kenshin reveals that he wields a unique reverse-blade sword (逆刃刀, sakabatō), which surprises her.
In a darker subplot, Takani Megumi, a woman forced into the harrowing life of producing opium for Kanryū, finds herself fleeing after witnessing the brutal murders of her fellow workers. Desperate for safety, she turns to the police for help, only to face a deadly pursuit led by Jin-e, who is in Kanryū's employ. In a shocking attack, he decimates the police station, but Megumi narrowly escapes amidst the chaos.
Kaoru is drawn into conflict when she crosses paths with Jin-e, who has been committing murders that align with her dojo’s fighting style. Outmatched in their confrontation, Kaoru is injured. Just then, Kenshin appears as her savior, and Jin-e quickly recognizes him as the true Battōsai. As a swarm of police arrives, Kenshin seizes the opportunity to flee with Kaoru to ensure her safety. Once at her dojo, they find brief solace, but it isn’t long before a group of thugs working for Kanryū attempt to seize control of the dojo.
Kenshin showcases his strength by defeating them without fatality, but takes the fall for the incident, leading to his arrest - a move made to protect Kaoru's dojo. During his time in jail, Saitō, recognizing him, engages him in a brief skirmish, but Kenshin, steadfast in his vow to refrain from killing, refuses to assist the police. Following his release, Kaoru welcomes him back, confident that he is not the Battōsai who has brought dishonor to her dojo.
As they navigate this new reality, Megumi struggles for her life on the streets and finds refuge with Yahiko Myojin, who brings her to the dojo, extending kindness and safety. Meanwhile, Kaoru, wanting to foster camaraderie, treats them all to dinner at the Akabeko restaurant. However, the gathering is disrupted when Kanryū arrives, attempting to entice Kenshin to work for him, which Kenshin humbly declines. This prompts a challenge from Sagara Sanosuke, leading them to a confrontation outside.
As night falls, Jin-e embarks on a remorseless killing spree, leaving behind a trail of victims that horrify the community, stirring painful memories of Kenshin’s past as an assassin; specifically, a moment when he had witnessed the sorrow of a woman mourning a man whose life he had taken. Later that night, a masked figure associated with Kanryū warns Megumi of impending threats.
The situation escalates when the wells surrounding the dojo become tainted with rat poison, suspecting Kanryū's interference. Utilizing her medical skills, Megumi works tirelessly to aid the afflicted. Angered and seeking revenge, she attempts to kill Kanryū but is captured instead. Recognizing the urgency, Kenshin and Sanosuke storm Kanryū’s mansion, assisted by Saitō in a chaotic confrontation that reveals Kanryū’s ruthless intent, armed with a Gatling gun. In the thrill of battle, they rescue Megumi but face a new peril as Jin-e kidnaps Kaoru.
Kenshin’s pursuit of Jin-e takes a harrowing turn when Jin-e uses a unique technique that paralyzes Kaoru’s lungs, leading to a heart-wrenching ultimatum: to save her, Kenshin must kill Jin-e. After an intense fight, Kenshin gains the upper hand but hesitates to deliver the final blow. In a critical moment, Kaoru overcomes her paralysis and implores Kenshin not to kill. In the end, Jin-e, defiant to the last, commits suicide, leaving behind a chilling message: > “He who lives by the sword must die by the sword," an echo of Kenshin's own vows against killing.
Exhausted and battered, Kenshin carries the unconscious Kaoru back to the safety of the dojo. When she awakens to find him absent, she embarks on a search, ultimately finding him returning with vegetables, a sign of his commitment to stay by her side and protect their newfound home.
