The story began when the Hitokiri Battousai killed a man named Kiyosato Akira. Although he was no match for the Battousai, his will to live and to return to his home town and see his fiancée was so strong that he managed to cut the Hitokiri before he died and leave him with a vertical scar on his left cheek. As he died, he tried to speak the name of his fiancée, but he never finished...

Himura Kenshin and Yukishiro Tomoe first meet in a teahouse in Kyoto. Tomoe comes and sits down next to Kenshin while he is eating and orders a cup of cold sake. Since she's a woman drinking alone, several men come to bother her, asking her to join them. When she refuses, they get angry and would have hurt her, but Kenshin intervenes. He pays for his food and leaves before Tomoe can say anything.

Outside, someone is waiting for Kenshin and he is ambushed on his way home. The assassin catches Kenshin in the chain attached to the end of his sword and pins his arms.

Meanwhile, as the assassin is preparing to kill Kenshin, Tomoe had left the teahouse and was following him in order to thank him for saving her. She comes upon them just as Kenshin breaks free and cuts the assassin in half with his own sword. The blood of the man flies and splatters on the both of them. Tomoe never blinks. She says to Kenshin that she came to thank him only to discover that he is the one responsible for all the blood raining in Kyoto. Then, she promptly faints into his arms.

Kenshin is shocked. No one is ever supposed to see a hitokiri kill and he doesn't know what to do with the woman. He doesn't want to kill her, but he can't leave her as a witness, so he does the only thing he can. He takes her back to his room at the Kohagi inn, the headquarters of the Ishin Shishi. He tries to sneak quietly in, but the innkeeper, Okami, is still awake and she sees Kenshin come in with the girl and she offers to give the girl a bath and a change of clothes while Kenshin goes off to his room. One other person also sees Kenshin arrive with the unconscious woman, an Ishin Shishi named Iidzuka.

When Kenshin wakes up in the morning, he finds the girl gone. He also finds that Iidzuka has been spreading rumours about what happened between him and the woman last night and he doesn't take the teasing well. He finds the woman in the kitchen helping Okami make breakfast and he tells her that he desperately needs to talk to her right away, but she tells him he'll have to wait because she's busy. She also finally introduces herself to him as Yukishiro Tomoe.

Although he wants to talk to Tomoe, Kenshin has to go and report what happened to his boss, Kogoro Katsura. Kenshin tells him about the shogunate assassin who ambushed him and Kogoro is disturbed. He knows that, somehow, their enemies have learned about the existence of Hitokiri Battousai which can only mean one thing. There is a spy among the Ishin Shishi.

After the meeting, Kenshin finally manages to track Tomoe down to speak with her. He asks her to promise that she would forget everything that happened last night. He tells her it would be best if she just went home to her family, but Tomoe answers that she has no family. Kenshin says that he doesn't know what her life is like, but he can't deal with her. Bitterly, Tomoe asks why he doesn't just kill her, but Kenshin tells her that he kills for the new era and for peace, not because he likes to. He would never kill an unarmed person. Tomoe asks him what he would do if she had a sword in her hand. Would he kill her? When Kenshin doesn't answer, she suggests that when the day comes that he knows the answer, he should come and tell her, implying that she isn't going anywhere.

Sometime later, Kogoro Katsura realizes just how much influence Tomoe is beginning to have on Kenshin and he tries to explain to her the cause of the Ishin Shishi. They are trying to throw Japan into chaos because only complete chaos can topple a government that lasted for three hundred years (Tokugawa) and allow a new era to be built. He says that Kenshin has been given the cruelest task, to be the Guardian of Chaos.

The next day, Tomoe is still thinking about what Kogoro Katsura told her. She goes to the room she shares with Kenshin and finds him asleep in the window seat. Looking at him like that, she finds it hard to believe that he is such a cold-blooded killer. She moves to drape her shawl over him as he sleeps, but he wakes up. Half asleep, Kenshin grabs his "attacker" and holds his sword to their neck. When he realizes it is Tomoe, he is horrified and he pushes her away. He is angry at himself because even though he told her he would never kill an unarmed person, he almost did. He tells her to get away from him or else he may end up hurting her, but Tomoe refuses. She says that Kenshin needs her to be "a sheath for his madness" and that he should let her stay. Kenshin can't understand her concern for him after he nearly killed her, but, after a moment, he tells her that the answer to her question - if she were holding a sword, would he kill her - is no. He could never hurt her. Not ever.

A short time later, the fragile peace that Kenshin and Tomoe were beginning to build is shattered. The Shogunate army, 20 000 men strong to Ishin Shishi's 3000 attacks Kyoto. The Kohagi inn burns to the ground and it is no longer safe for the Ishin Shishi to stay in Kyoto. Kogoro Katsura tells Kenshin that he has prepared a cottage in the countryside for him. He says that if Tomoe has nowhere to go that she should stay with him because a young married couple is much less suspicious than a young man alone. Standing together, Kenshin says to Tomoe that it would be best for them to live together. He doesn't know what may happen between them, but he doesn't want their relationship to be nothing more than a disguise. he wants it to be just the two of them together "until death do us part."

The two, now married, go into hiding in the countryside. Iidzuka, Kenshin contact with the Ishin Shishi, comes and brings him news of the goings on in Kyoto and the Shinsengumi. Iidzuka says that he is surprised that Kenshin hasn't gotten bored out in the middle of nowhere, but Kenshin replies that he doesn't miss the excitement. He never enjoyed killing people. Returning home from his meeting to see children playing in his yard, Kenshin realizes that, for the first time in his life, he is truly happy living with Tomoe. This is what he was fighting for.

Meanwhile, back in Kyoto, another Ishin Shishi, Katagai, sees Iidzuka in a crowd. He is surprised to see him back so soon because he knows Iidzuka went to see Kenshin and was planning on spending the night at his house. He follows Iidzuka to a meeting with the Yaminobu, a group of Tokugawa ninja. It seems that Iidzuka is the spy they have been looking for. Katagai tries to go and warn Kenshin, but he is caught and killed and the Yaminobu send out their agent, Tomoe's little brother Enishi, to put their plan into action.

Tomoe is shocked to see her little brother arrive at her house since no one is supposed to know where she and Kenshin are, but when he speaks, she knows how he found out. He tells her that it is finally time to get her revenge on the Hitokiri Battousai for killing her fiancé, Akira, that it is time for her to report to the Yaminobu and tell them Kenshin's weakness so they can kill him for her. But, far from being happy, Tomoe tells Enishi to leave. Enishi can't understand why Tomoe would want to protect the man who caused her such unhappiness and he leaves in a rage. Kenshin sees him storming out and he asks where Enishi is going. Tomoe says that he is going back to Edo. She realizes that she has never told Kenshin anything about herself or her past and she thinks that she would like to tell him.

Tomoe tells Kenshin about the death of her mother and how she raised Enishi herself. She tells him how she was descended from a Shogunate samurai family and how she was engaged to the successor of another family. She says that because she was never able to show her fiancé love, he left her to go to Kyoto where he died. She didn't tell Kenshin he was the one who killed the man. She begins to cry, blaming herself for not being able to smile or cry or say anything to prevent her fiancé from leaving. She believes it is her fault he died.

Kenshin, not knowing what else to do, only holds her in his arms. He tells her about his own past, about how he left his master to become a hitokiri, truly believing that he could use his sword to bring about a new era, but it seems to him that no matter how many he kills, Japan gets no closer to peace. He says that living with Tomoe has shown him what happiness and what protecting someone means and that even if he can't protect everyone or make everyone happy now, someday, when the hitokiri is no longer needed, he will find a way to do it without killing in order to atone for all the lives he destroyed. Until then, he vows to protect Tomoe and make her happy. With those words, Tomoe smiles at him for the first time.

In the morning, Tomoe decides that she has to go and meet with the Yaminobu. Looking at him, she can forgive him for taking away her happiness when he killed Akira because he gave her new happiness. She can forgive him for all the people he killed because she knows that he will save many more lives than he has taken. She leaves while Kenshin is still asleep.

Tomoe enters the Kekkai Forest, the base of the Yaminobu, with the plan to give them a false report. When the leader asks her what weakness of the Battousai's she has discovered, Tomoe lies and tells the ninja that Kenshin's weakness is to be attacked while sleeping. The leader is not convinced and, suddenly, he asks Tomoe if Kenshin loves her. Tomoe doesn't understand, but the leader continues, saying that if the Hitokiri Battousai does love her, he will answer the challenge letter that Enishi has been sent to deliver. Tomoe has become bait for their trap.

Realizing that she has been tricked, she pulls a dagger and tries to kill the ninja leader, but he knocks her unconscious with one blow and tells his men to prepare for Kenshin's arrival.

Kenshin goes to the Kekkai Forest to fight, but he quickly learns that the advantage belongs to the ninja. The spirits of the forest have created a barrier that prevents him from sensing his opponents' moves. Furthermore, as Kenshin fights his way through the Yaminobu's stronghold, the ninja set off explosives that nearly blind and deafen him. Although he manages to kill them all, he is seriously disadvantaged when he arrives to fight their leader.

Meanwhile, Tomoe regains consciousness to the sound of men fighting. She looks around on the floor of the shack she is in and picks up her dagger. Peering outside, she sees a badly wounded Kenshin and the Yaminobu leader fighting. Tomoe vows that she will not let someone she loves die again and she goes out to stop the fight.

Half blind and deaf, delirious from blood loss and cold, Kenshin knows he is going to lose the fight. With that thought in mind, he prepares to launch one more attack in the hopes of taking his enemy with him, but as he strikes, he smells the familiar perfume of white plums that Tomoe always wears. By the time he realizes that she has put herself between him and the ninja, it is too late to pull his attack. His sword slices through her to stab the Yaminobu in the heart. As she falls, Tomoe's dagger cuts Kenshin's cheek, completing with a horizontal slash, the cross scar that her fiancé had started in Kyoto so long ago.

Kenshin holds Tomoe in his arms, knowing that she is dying because of him and that there is nothing he can do to save her. Gently, Tomoe reaches up and touches his scar. She tries to tell him that it is better that it end this way and so he shouldn't cry, but she only smiles, her second and final smile before she dies. Kenshin can only think that he should have died instead of her.

Two weeks after Tomoe died, Kenshin was still sitting at home, depressed, when he saw her diary. He picks up the little book and begins to read the first entry only to learn that the man he killed so long ago who scarred his face was Tomoe's fiancé, Kiyosato Akira. It was her name the man was trying to speak before Kenshin stabbed him in the heart. He is devasted to learn that, after all he promised her about protecting her happiness, he was the one who took it away from her in the first place.

Kogoro Katsura returns and tells Kenshin that he is no longer needed as a hitokiri. Another man, Shishio Makoto, will replace him and has already been sent to deal with the traitor. He wishes Kenshin to return to Kyoto and guard the members of the Ishin Shishi against the Shinsengumi. As Kenshin stands outside with Kogoro, the children come up to him and ask him to play. Kenshin says to Kogoro that he will go to Kyoto because if he quit fighting now, then all the lives he had taken would have been wasted. He will continue to fight to build the new era, but when it comes, he will never kill again. Then, he turns to the children and tells them he will play with them until nightfall.

Himura Kenshin, the Hitokiri Battousai, returned to Kyoto and fought the Shinsengumi, but when the war was over, he disappeared...only to emerge eleven years later in Tokyo as the wandering rurouni Kenshin....