Himura Shinta is born into a peasant class family on June 20.

An epidemic sweeping through Shinta's village causes his parents to die of cholera. After his parents' death, a group of slave traders somehow gain custody of Shinta.

The slave traders who have custody of Shinta are murdered by a group of bandits with whom they had crossed paths while on journey with a shipment of slaves to an unknown destination. Luckily for Shinta, a swordsman passing by the scene of the murders, defeat the bandits before they could kill Shinta too. The swordsman's name is Hiko Seijuro, the thirteenth inheritor of the Hiten Mitsurugi school of kenjustu.

Before leaving, Hiko instructs the Shinta to go to the next village to receive help and report the murders of whom Hiko thought to be the boy's parents. He continues to tell Shinta that tragedies similar to his are happening all over Japan due to the war. He should just be happy that he is still alive. Shinta does not look at or respond to Hiko. He simply remains kneeling on the ground looking at the dead bodies which lay before him.

Several days pass and Hiko inquires at a sake shop whether a boy has come to the village. The store owner tells Hiko that no one has come to the village. Hiko leaves the store and arrives to a clearing where he sees a field of hand crafted wooden crosses. In midst of the crosses, the young boy is standing in front of three graves marked with stones. Hiko asks Shinta if he dug graves for the bandits that murdered his parents too. Shinta tells him that they were not his parents but slave traders. However, there is no difference who you were once you die, therefore he dug the graves for them. Hiko asks him who the three headstones belong to. Shinta tells Hiko that those headstones belong to Akane-san, Sakura-san and Kasumi-san, three sisters who were sold to pay off their family debt. Even if it would have costed him his life, he wanted to protect them because he was the only boy amongst them.

Admiring the boy's integrity, Hiko decides to take Shinta into his care, declaring Shinta to be his pupil and successor. Since the name Shinta was too "sweet" for a swordsman, he changes Shinta's name to Kenshin (ken = sword; shin = heart), which was much more fitting for a warrior. From that day forth, Kenshin would begin his training of the Hiten Mitsurugi school.

Kenshin seeks permission from his master Hiko Seijuro to let him leave and use the Hiten Mitsurugi Ryu he has learned to protect the innocent people suffering from the chaos of war. Hiko tells him no, saying that Kenshin's training should be his only priority and that outside affairs are not to be his concern. However, Kenshin remains firm to his belief and he can not understand his master's reasoning for not letting him leave. The two get into a heated dispute which is left unresolved as Kenshin decides to leave his master to pursue his own destiny.

Not too long after his departure, Kenshin is discovered by Katsura Kogoro and Takasugi Shinsaku during the recruitment activities to form an anti-shogunate group of warriors called The Kiheitai. After witnessing the power of Kenshin's "Hiten Mitsurugi Ryu - So Ryu Sen", Kogoro orders Shinsaku to bring the boy back to Kyoto with them.

That very night, the two men arrange to meet with Kenshin. Kogoro asks Kenshin if he has ever killed a human using Hiten Mitsurugi Ryu. Kenshin replies that he has never killed before. Kogoro continues to ask him if he could kill a person. Kenshin responds by saying that if a new era could be born which will allow the people to live in peace in return for him taking lives that may fall victim to his blood-stained sword then he would do so. Kogoro decides to designate Kenshin as a hitokiri for the Ishinshishi. However, Shinsaku warns Kogoro that using such a young boy to fulfill the cruel duties of an assassin will surely destroy the boy's life. Thus at the tender age of fourteen, that night marked the birth of Choshu Ishinshishi, Himura Battousai!