The Cross-Shaped Scar
Kenshin's search for peace and forgiveness began just before the realization of the Meiji government he fought so hard for. The Ishin Shishi had hired him as a killer, but Kenshin was only just a boy, no matter how good he was with the sword. He eventually becomes lost in the violence, suffering from a minor sort of madness because of all that he had done. He wrapped up Himura Kenshin and buried him in his heart while he kept on killing as the fearsome Hitokiri Battousai.
It was at this time that he crossed paths with a certain Kiyosato, who is neither important, nor terribly skilled but, due to a twist of fate, accompanies one of Kenshin's assigned targets. Though his companions all fall at once, Kiyosato's will to live drives him to fight, harder than perhaps he thought he could. He manages to give Kenshin the first half of the cross-scar on his cheek during their duel, and whispers a name before he dies. Before this, Kenshin had perhaps been standing on the edge of a precipice, and with this, he takes the first blind step off it, and spirals down into a sort of depression, where he found that everything tasted foul, and his hands perpetually smelled of blood. Until Kiyosato, he had been killing people willing to die for what they believed in. Kiyosato was the exact opposite: he wanted to live, more than anything. Taking that life perhaps drove home to Kenshin that what he was doing -- as glorious as his reasons may be -- was murder, pure and simple.
Kenshin hits rock bottom when, some time later, after defending a young woman from some lecherous drunks in a tavern, he is ambushed by an assassin working for the other side. Kenshin dispatches of the man accordingly, however the woman from the tavern has witnessed the act. For a moment, in a rain of blood, his soul seems to hang in the balance, as he debates what to do: to kill or not to kill this innocent witness who has followed him to give him nothing but her thanks.
But when she faints into his arms, he can't seem to bring himself to kill her and takes her back to the Ishin Shishi headquarters instead. The woman, Yukishiro Tomoe, insinuates herself into the inn's day-to-day life and doesn't seem to mind that people assume that she is Himura's girlfriend. She is puzzling to Kenshin in at least three ways. First, he wonders why she doesn't just go home. Then he wonders why he did not kill her, and then he realizes that he simply could not. Most of all, she asks him the question that forces him to rethink (or remember) the reason why he killed, and if he intended to keep on killing, blindly, for long.
The two of them settle into an easy companionship, marred once when Kenshin, mistaking Tomoe for an attacker, wakes up and points his sword at her throat. Eventually, however, Kenshin begins to trust Tomoe, to the point where he peacefully sleeps and lets his guard down around her. Their life together gets an unanticipated push forward when, following the infamous incident in the Ikedaya inn and the subsequent (though momentary) defeat of the Ishin Shishi at the hands of the Bakufu, Kenshin and Tomoe are forced to go into hiding, under the guise of a young married couple, though Kenshin did say the marriage need not be for show.
They settle into a quiet life together, in the countryside, where we are given a glimpse of what Kenshin will eventually be: a quiet man who gets along well with children, who is at ease just playing, without a sign of darkness or evil at all. It is during those months that he realizes what happiness is, and understands for the first time what he has been fighting (killing) for for so long. Still, all good things must come to an end, and Kenshin and Tomoe's new-found happiness is brought up short by the arrival of a boy, Yukishiro Enishi, Tomoe's younger brother.
It is immediately revealed (in a private conversation between brother and sister) that there is a plot to kill Battousai, and the key to that plot is none other than Tomoe herself. Later, after sending Enishi off and revealing her feelings to Kenshin (how she had unexpectedly found happiness with him), Tomoe leaves a sleeping Kenshin behind to rendezvous with the assassins. She attempts to lie to save Kenshin, whom she has come to love, but to no avail. For, in sending her to find his weakness, she has unwittingly become it, and the assassins use her as bait to draw Battousai out.
Kenshin, only just partially recovered from the madness of an assassin, is driven berserk by his desire to save Tomoe and goes hitokiri on all of their butts. In the final fight with the last assassin (all others having been slain, dismembered, or scared witless and sent fleeing), a severely injured and sensationally handicapped (literally, without his senses of sight, hearing, or spider-sense) Kenshin is at a clear disadvantage but still intent on killing them all. Tomoe, afraid of losing the man she loves yet again, runs between Kenshin and his opponent in a crucial moment...and dies when Kenshin unintentionally hacks through her as he is striking his opponent. But she doesn't die without giving Kenshin the second half of the cross-scar, when her knife comes flying out of her hand as she falls.
So Kenshin's cross-shaped scar is formed, given to him by lovers (for Kenshin soon learns that Tomoe was engaged to be married to Kiyosato), and sealed by his own guilt and remorse. So also begins the long and difficult path Kenshin will follow for the rest of his life: that of a man seeking redemption and forgiveness and who swears never to kill again.