The movie begins in the final days of the Tokugawa Shogumate, the Bakamatsu in Kyoto.  It’s night, the full moon shining down on a bamboo forest.  Hiding amongst the bamboo stalks, a dozen samurai await the orders of their leader.   They are all silent, awaiting the signal from their leader.  Suddenly, the leader shoots forward, rushing towards a house in the middle of the forest.  The samurai follow quickly and silently.

Meanwhile, opposing samurai come out of the house, their swords drawn and ready.  The leader of the charging samurai draws his sword and charges straight towards the house.  Several of the opposing samurai are killed by his blade before they could even move.  After around four are killed in a matter of seconds, the rest of his warriors arrive and the battle ensues.  Then, the first of the leader’s men is killed, slashed down the face with a trademark broken sword at his side.  Two more of the leader’s men charge the samurai, only to end up dead.  The leader looks up to face the opposing samurai, a man with cold eyes and a cross shaped scar.  They ready themselves, waiting for each others moves.  Then, their swords come together.  A heated battle breaks out between the two, driving them into the forest.  The leader swings at his opponent, only to slice through bamboo stalks, for his opponent has leapt into the air.  His opponent comes down, and once again their swords clash.  The opponent has landed safely on the ground, the leader’s sword still in its defensive position.  At first, it looks as if it has come to a draw, until the leader’s sword breaks.  Blood spills from his body and he falls to the ground, dead.  The opponent opens his eyes as blood seeps down from a wound on his forehead.  A narrators voice appears and talks about the greatest fighter who ever lived as the Battousai walks into shadow.

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The next part of the story takes place in the year 1879, the twelfth year of the Meiji.  Kenshin and the others are busy enjoying a calming train ride to Yokohama in order to take in the sites.  When the train enters the station, everyone disembarks, heading for the main street.  Upon arriving, the Kenshin-gumi sees a young woman being harassed by a gang of Australian sailors who had just arrived in port and are drunk like there’s no tomorrow.   As they are preparing to help her, a young man steps in and beats the sailors with the help of Sano and Kenshin.  As police arrive, Kenshin and the man, who introduces himself as Shigure Takimi, run to hide their swords from the police, hiding in front of an old shrine.  Kenshin and Shigure introduce themselves, and Shigure says he’s honored to meet Kenshin.  They part ways, only for Kenshin to run into Saitoh, the ex leader of the Shinsingumi.  Saitoh warns Kenshin to stay away from Takimi, and walks off.  Kenshin returns to the others, only to see an embassy attacked, and the attackers getting away.  Yahiko is impressed by the general that appears to stop the attack, causing much taunting from Sano and Kaoru.

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Several days later, in Tokyo, the woman, whose name is Toki Takasuki, is dismissing children from her mansion from a lesson she had just taught.  Meanwhile, Kaoru is sweeping the front of her dojo while two girls, who we all know as Ayame and Suzume, are playing with their grandfather and a nice pair of pinwheels.  Toki arrives, wishing to speak with Kenshin, who is getting tofu for dinner, which it is no longer needed as Toki brought with her fish.  Kenshin comes home, only to find the tofu useless and that Toki wishes to speak with him.  Toki and Kenshin go the back yard in private, where Toki tells him that she is worried about Shigure, who left without telling her where with a comrade. She’s worried something is troubling him and wants Kenshin to speak with him, Kenshin accepts.  Yahiko ends up escorting Toki home, only to meet Shigure himself and another boy whose father had died in battle along with Yahiko’s father.  Shigure tells Yahiko to treat the mansion like his second home.

Yahiko heads out to practice with the boy everyday and Kenshin goes to visit Toki while she’s teaching to see if Shigure is home.  When he’s not, Kenshin asks that Toki tells him to meet Kenshin on the bridge at dusk.  Toki agrees and thanks him for his help.  Meanwhile, the general Yahiko admired, Captain Tomono, is speaking to his superior about extra protection along a parade route of an Englishmen who is visiting Japan.  What his superior doesn’t know is that Tomono is actually plotting the downfall of the superior, so he could become a higher rank, in a quick and flawless promotion.  The superior says that they will share duties of leading the guards, and Captain Tomono quickly agrees.

Meanwhile, ammo and guns are being loaded up and shipped to a shrine while Shigure watches almost proudly, waiting for the men to finish their work.  Shigure tells them that they will strike when the Englishmen arrives in two days.  Upon returning home, Shigure insists that he and Toki eat dinner together, where Shigure says that he’ll be leaving her soon.  Toki once again starts worrying.  Shigure then leaves to meet Kenshin on the bridge as planned, just as snow begins to fall on the ground.  They talk, and then as a fight breaks out, Shigure disappears into thin air. 

As this is going on, Sano is talking about Shigure’s history with a group called the Izu Clan with a close friend.  His friend tells Sano things rather vital to help Shigure, and then Sano rushes off to tell Kenshin.  Yahiko, who is on his way home, sees his friend with a gang of men that are following Shigure.  Curious, Yahiko follows them.  They lead him to the shrine where the guns and ammo are stored, and Yahiko listens as Shigure tells his plans to his followers.  Yahiko is discovered and almost killed when he says he wants to fight along side Shigure and the others.  They let him.

Meanwhile, Kenshin and Sano meet up with Toki to find where Shigure is, only to find that see doesn’t know and Kaoru comes by to say that Yahiko hasn’t turned up yet.  Worried, they go out to look for them.  Saitoh walks on his own to a shrine where he finds a dead spy of his.  Angrily he puffs his cigarette and looks at the sky.  Shigure’s group trudges forward and stops at a dock where several boats are parked, Shigure then calls Yahiko to him, punching him in the stomach and rendering him unconscious.  He leaves Yahiko in the boat house and they leave, as Shigure’s comrade runs off to get information about the parade.  Unknown to Shigure, his comrade gets info from Captain Tomono himself, and that they are just using Shigure so Tomono gets promoted, even at the expense of Shigure’s life.

The next morning, the Kenshin-gumi and Toki arrive back at the mansion in defeat, only to see Yahiko walking towards them, leaning on his Shinai for support.  Angry, Kaoru slaps him and then hugs him, crying on his shoulder before Yahiko admits that he didn’t know where Shigure was going; all he knew was that Shigure said something about an ambassador from England.    Kenshin automatically knows what’s going on and heads straight to the embassy.  However, the attack starts before Kenshin even arrives, claiming many men, soldiers and patriots, including However, the attack starts before Kenshin even arrives, claiming many men, soldiers and patriots, including Yahiko’s friend.  Kenshin arrives just in time to stop Shigure from killing the ambassador, they fight, and Shigure then recognizes him from somewhere.  Shigure runs off, leaving a disgruntled Kenshin behind.  Kaoru, Yahiko and Toki arrive at the scene to see the destruction.  Toki cries and Kaoru walks over to Kenshin as he talks about his part in the war.  Kenshin then gains permission to speak with Shigure before the soldiers’ attack where the rebels are hiding, hoping to end it all peacefully.

When Toki confronts Kenshin and says that Shigure is going to die, Kenshin promises to help and tells Kaoru that he himself, as the Hitokiri Battousai had killed Toki’s brother, the reason Shigure lead the rebels to the attack.  Kenshin and Sano go to where they are hiding, seeing Shigure has barricaded himself inside.  Sano breaks through the barrier and allows them to go through.  After a brief scuffle, Kenshin and Shigure begin to fight.  Shigure is still in pain about how the Meiji government has made fun of Gentatsu and the other soldiers on his side.  Shigure and Kenshin begin to fight, Kenshin coming out victorious, only because Toki arrived, hugging onto Shigure and telling him to stop. Shigure surrenders, agreeing to allow the soldiers to arrest him.  However, Captain Tomono has other plans and orders his men to open fire on them, killing Shigure as he shields Toki from the bullets.  Angry, Kenshin reverts to Battousai, attacking and injuring Captain Tomono, but is saved from being shot when Tomono’s superior arrives, telling to soldiers to leave Kenshin alone and to place Tomono under arrest.  As it turns out, Saitoh had found out about what happened and had told them.  Kenshin and the others watch sadly as Toki pines over Shigure’s still body.

Several days later, Toki is once again seeing the children off as Kenshin appears to have tea and to talk to her.  During so, Kenshin tells Toki that it was him who killed Gentatsu.  Toki says she understands, and decides to leave Tokyo to visit her brother’s and his comrades’ graves.  Kenshin and the others see her off as she walks down the road alone, but Shigure’s soul watching over her.