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Samurai X is a fictional anime based on Historical events during the Meiji Era. It all begins when a group of people are traveling to another town with a young boy named Shinta. The group is murdered by bandits. However, before Shinta is killed, a sword's master by the name of Seijuro Hiko saves him. He returns later that day to find that the young boy has buried all the bodies by himself. Shinta feels regret for not being able to protect the people that were murdered because he was just a boy. That is when Hiko offers to train Shinta to be able to protect people. Shinta accepts. As a result, he is given the name Kenshin, an appropriate name for a swordsman.

It is now the start of the Boshin War; Kenshin is upset by the deaths of inocent people. Ironically, he leaves his training to become an assasin for the Choshu clan. As an assasin, Kenshin is forced to kill a bodyguard of the Shinsengumi named Kiyosato Akira. A few days before, Kiyosato had left his Fiance, Tomoe Yukishiro, with the promise of returning. His will was immensly strong that he repeated her name until his death. In the end, he managed to cut Kenshin, leaving a slash mark in his face.

Before Kenshin is able to return home, he is attacked by an assasin. At this very moment, Tomoe, who left her home in search for her husband's murderer, appears before Kenshin, drunk and splashed with blood. Kenshin is bewildered, but soon decides to take her back to the Inn where he recides.

Their stay in Kyoto is brief. News of Kyoto about to be set on fire and the discovery of the assasin's identity leave Kenshin and Tomoe in danger. Katsura, the owner of the Inn where Kenshin is staying arranges for them to be sent to a near town to live as husband and wife.

Time flies and soon Tomoe finds trust in the man she knows killed her fiance. Unfortunately, her younger brother Enishi visits to tell Tomoe that the Shinsengumi's assasins are close by and that she will soon be able to avenge Kiyosato. That night, Tomoe realizes that she is in love with Kenshin and must stop the Shinsengumi before they kill him. She leaves home before Kenshin awakes to try to dissuade the Shinsengumi from killing Kenshin. She is told that she is a terryble being for falling in love with the man who distroyed her happyness and assasinated her childhood love. Tomoe tries to comit suicide by slicing her tongue and bleeding to death, but is stoped.

Meanwhile, Kenshin is visited by a trusted man, who actually is a spy for the Shinsengumi. He tells him that Tomoe has left with him to join the men who are trying to assasinate him, because Kenshin killed her fiance. Shocked, Kenshin rushes to find Tomoe and is attacked by three agents; he is badly injured. When he finally reaches the final agent, he is kicked around and almost killed. Seeing that, Tomoe rushes to them and stops the assasin's sword before it kills Kenshin. At that exact moment, Kenshin slices through both of them, killing his first love.

Before her death, Tomoe cut's Kenshin's second line. Therefore, giving him the final wound of his X-shaped scar. Kenshin then promises to protect the inocent without taking another life.