Kenshin was born Shinta, a child of peasants of the farmer class, who died of cholera when he was 7. Shortly afterwards, he was sold into slavery, meeting three sisters - Kasumi, Akane, and Sakura - who had been taken as payments for debts. When bandits attacked the slave caravan, the sisters attempted to protect Shinta, shielding him with their bodies and begging for him to be spared, only for them to be cut down in front of his eyes. However, before the bandits could finish the job, Hiko Seijuuro the 13th passed by the caravan, and killed all the bandits, leaving young Shinta the only one left alive. After telling Shinta of a village a short distance away, Hiko left.
When he returned, after learning that no child had come to the village, Hiko returned to the place of slaughter, expecting to find just one more body to bury - only to discover that Shinta had already buried all the bodies – sisters, slavers and bandits, answering to Hiko’s query of why he had done it that it didn’t matter what had happened when they were alive, once they were dead they were just bodies. Hiko, impressed, poured sake on the stones that marked the graves of the sisters ,and took Shinta as his pupil, changing his name to ‘Kenshin’.
Hiko raises Kenshin and teaches him the art of Hiten Mitsurugi Ryu. At age 14, however, Kenshin gets involved with the revolutionary movement, and joins the Kiheitai, against Hiko’s wishes, leading to a break between them. In the Kiheitai, his prodigious skills with the sword catch the attention of the Ishin Shishi’s commander Katsura Kogorou, leading to him going to Kyoto to become the Ishin Shishi’s main Hitokiri. As a Hitokiri, Kenshin was ruthless, cold and utterly lethal, and his mastery of all forms of Battoujutsu led to him being given the name “Hitokiri Battousai’. However, behind the cold mask of a hitokiri, there was still a young, idealistic boy, who was slowly going mad from the bloodshed – until he met Yukishiro Tomoe.
After saving her from some ruffians in a pub, he leaves, only to get into a fight with a shogunate assassin. Eventually he wins, cutting the man in half from head to toe, causing the blood to splatter on Tomoe, who had followed him to thank him, and leading to the immortal line – ‘you are the one who makes it rain blood’. After she faints, Kenshin carries her back to the inn that is the Ishin Shishi headquarters.
The next morning, he wakes up to discover that she has left, and races down to find her – only to face plant on the floor at the sight of her calmly doing chores. The tone of their relationship is set.
Tomoe treats him like a human being, gently teasing him, and asking him questions that make him think beyond his stubborn insistence of the rightness of what he was doing, which eventually leads to a time when Tomoe walks in on him sleeping in their room, and goes to put her shawl around him, causing him to wake up and attack her on instinct, barely stopping himself from killing her. This, instead of scaring her off, causes her to say that he needs a ‘sheath for his madness’, and she offers to stay with him, leading to him swearing that he will not kill her, no matter what – never her.
However, during this time, the Ishin Shishi is virtually split in two when the decision to light Kyoto ablaze causes a famous conflict with the deadly "Wolves of Mibu", the Shinsengumi, and after the crisis suffered by the Chōshū clan in the Ikedaya incident, Katsura orders Kenshin and Tomoe to abandon Kyoto and flee to a remote village. He also orders them to put on the facade of a pair of pharmacists, as husband and wife, however, Kenshin doesn't like the idea of pretending, and proposes for real – and Tomoe accepts.
As husband and wife, they live happily in Otsu together, causing Kenshin to finally realise what real happiness is, as he plays with the neighbourhood children, uses plants and herbs to help people’s sickness and injuries, and comes home every night to his wife.
However, Tomoe's younger brother, Yukishiro Enishi, manages to find what was supposed to be their hidden location. This seems to spur Tomoe towards sharing her past with him for the first time, telling him of her murdered fiancee, who left because he couldn’t tell that she loved him, and wanted to become a warrior of repute in order to impress her. Kenshin embraces her and allows her to cry on him, before telling her of his own past, leading to a mental and emotional consummation that hadn’t been there before.
Kenshin then tells her that he will continue to be an assassin until the Revolution is over, but will find a way to repay those whose lives he destroyed, and he tells her that he wishes to protect her happiness which Tomoe returns with a yes and a genuine (and her first) smile.
That night, Kenshin sleeps the night through in the same bed as Tomoe for the first time.
The next morning, Tomoe meets with the leader of the Yaminobu, a pro-Shogunate covert network of ninjas that had formulated a plan to assassinate Kenshin. She had originally joined them to get revenge on Kenshin for killing her fiancé, but had eventually fallen in love with him, and decided to try to call it off – however, despite her lying about his weakness, the leader of the Yaminobu reveals that all along they had actually used her to create Kenshin's weakness.
Meanwhile, Kenshin receives a ransom note, and goes off to find his wife, but is ambushed by Yaminobu ninjas and is severely wounded. He manages to defeat them and eventually finds the leader of the Yaminobu. Meanwhile Tomoe, having woken from being knocked out by the leader and realised what was happening, had made a last ditch attempt to save Kenshin by jumping in between the two warriors to both stab the Yaminobu leader with her tanto, and also protect Kenshin from any more harm. At the same time, Kenshin, his senses badly damaged, had put his all into a last strike – and ends up killing both Tomoe and the Yaminobu leader. As she falls, Tomoe's knife flies into the air and coincidentally slashes Kenshin's already scarred cheek, creating the famous X-shaped scar across his left cheek. Later, Kenshin reads Tomoe’s diary, and finds out the truth – that he was the one to kill her fiancé. This is when he makes his vow never to kill again.
Following the death of Tomoe, Shishio Makoto replaces Kenshin in his role as assassin, and Kenshin is reassigned as a guerrilla swordsman protecting the Imperialists. After the end of the Bakumatsu, after the battle of Toba Fushimi, Kenshin leaves Kyoto, being met on his way by the swordmaker Arai Shakku, who gives Kenshin the sakabatou, the reverse-edged sword.