So long ago, so many nights, so many storms, so many blood. Years ago in Japan, an old man stares at a picture of him flanked by three young men, presumably his sons. Pulling a dagger out of the box, the old man looks at it intently and says ‘it is yours.’ His son asks what is his – the first seat of his house, the Kaishek dominion, Clan Yashida? What is his? Clutching his chest, the old man tells his son Yolyn to stop for at last it is his. Holding the bloody dagger, Yolyn watches his father die at his hand.
Today, in Japan, at the grave of Lady Mariko at the House Yashida compound, Logan recalls the events of the night that she died. After being poisoned by Matsuo, she lay in Logan’s arms. Logan pleaded with her to let him take her to the hospital to obtain the antidote but Mariko informed him there was none. Weakly, she then told him to not let her enemies take her life and to accept the only thing she has left to give. When Logan said he didn’t, Mariko told her love to release her with his claws. Initially, Logan declined but, when Mariko informed him that the poison kills too slowly and that it burned, Logan did the only think he could and released her from her misery.
From behind him, a man exits a house on the compound and calls out to Lady Mariko Yashida, a braver or purer soul never existed. Turning around, Logan mentions to Kenuichio Harada that he didn’t know he cared. Harada proceeds to tell Logan that he should have called. He is welcome to visit his half-sister’s grave whenever he wishes. There’s no need to scale the wall.
Logan replies that he didn’t feel like disturbing the Silver Samurai’s important business. A criminal empire doesn’t run itself. Anyway, it doesn’t seem like anyone would have came if he’d knocked. Holding up a beer, Harada chuckles and says that he supposes you could say Clan Yashida has been “downsized” as they say in the West. When he offers Logan a drink, it is declined. Logan then asks him if he normally visits his sister’s grave loaded at the crack o’ dawn. Harada replies that she would know that he means no disrespect. Mariko led the Clan before him and understood the pressures of its leadership. Lighting up a cigar, Logan remarks that she understood it so well it got her killed.
Harada agrees and points out that she was trying to free the clan from its criminal ties but freedom from the Yakuza and the Hand is an unlikely venture. At least she left this world with her soul intact. He then tells Logan that he often thinks of her. Every crime boss in Japan thought they could bully Lord Shingen’s timid little daughter into expanding their territories. She stood her ground, even in the face of death. Once, he tried to force her into giving him complete control of the clan but she told him to ‘do what he must’ when his sword was at her throat. She held everything he ever wanted in her hands and was trying to give it away, just not to him.
Logan remarks that he got his empire when she died though, dint’ he? Harada states that he did but only now does he see why she registered his campaign for clan leadership. He believes, in some way, she was trying to protect him. Sighing, he adds that the clan’s corruption is too deeply seeded. Eventually, she would have realized the futility of trying to purge its vices. Eventually, she would have realized there are worse things than the Yakuza. It’s better Mariko died before she was twisted into some puppet like he has.
Enraged, Logan asks Harada how it was better and slaps him across the face. As he does, he tells him that his change of heart is a little late for Mariko and asks him if life is lonely atop the criminal dung pile? It’s easy to have second thoughts when everything’s gone into the toilet. Mariko was alone too. Where was the Silver Samurai when she… Harada replies that he was there; he fought for her the day Matsuo had her poisoned. Walking away, Logan tells him that he fought for himself. He threw his Clan back into the cesspool, undoing everything she died for. He then tells Harada that he made his bed, now die in it.
Watching the compound through a scope, a large man with platted hair is informed by one of his men that the short westerner is leaving. The man remarks that watching Haan’s insubordinate samurai may yet bear fruit especially if the westerner is who he thinks he is. His female associate asks that, if he is the mutant warrior, how do they get him to help them? The large man replies that the Wolverine considers himself to be an honorable man, a hero. She is told that all honest and noble men have weaknesses which can be used against them.
At a penthouse in another section of Japan, Logan visits his old friend Yukio. When she answers the door, she tells him he’s late. Logan apologizes and then mentions that he likes the new pad. Beats the ‘poor ronin’ act, don’t it? Yukio tells him that she’s a woman of many talents. Making a little economic improvement happen wasn’t difficult. After Logan replies that he bets, Yukio inquires if the present he is holding is for her. Logan tells her it’s a little something for Amiko and proceeds to ask where she is. Yukio informs him that she should be on her way home from school. If they hurry, they could meet her.
Walking down the street, Yukio tells Logan that life is good. Better than she’d guessed it would be after he gave her Amiko to look after. Who would’ve thought that she has maternal instinct as well as killer instinct? He won’t believe how much Amiko’s changed. She’s really come out of her shell. Lots of new friends, a few problems with some bullies but that worked itself out. Logan says good and that he can’t wait to see her, he’s been away too long. Yukio warns him to just be prepared for a little adolescent attitude.
When Logan asks yeah, Yukio asks can he blame her. After her mother died, she put him on a pedestal, he promised to watch over her. She thinks his long absences… Logan finishes her thought ‘have hurt her.’ He states that he wanted to see her but his responsibilities to the X-Men always pull him away. They’re just pullin’ through some bad times. He wasn’t himself. Apocalypse transformed him into his Horsemen of Death, bonded adamantium to his skeleton to make him unstoppable and unbreakable. He managed to shatter Apocalypse’s hold on him but not before Cyclops gave his life to stop him. It’s been six months but the hurt, an’ the guilt, won’t go away. Summers an’ him never saw eye to eye but he respected him. Now he’s gone an’ he’s not sure if he shouldn’t share some o’ the blame. Yukio tells him that Scott Summers knew the risks of being an X-Man, same as he does. It was his time, best to leave it at that.
Passing by a tea house, Yukio recommends that they stop in there. Sometimes Amiko hangs out with her friends there. Looking around, Logan points out that the neighborhood they’re walking through is pretty bad. She doesn’t let the kid walk home this way, does she? Yukio asks him why not, it’s safe? Just then, a man crashes through the window of the tea house and onto the street in front of Logan and Yukio. Standing on the broken windowsill, Amiko is wearing a leather jacket and a skull cap with her fist balled up and bloodied.
Scared half to death, Amiko asks Yukio what she is doing there. Yukio angrily yells at her. “Never again Yukio, I’ve learned my lesson Yukio, I didn’t mean to break his arm Yukio.” She thought they were done with this stuff. She’s not showing her another thing until she… Amiko cuts her off and tells her to wait and listen to her. That old slime ball was all over Sukie and wouldn’t get away. No one was helping so…
Taking a knife from the man Amiko punched out, Logan tells Yukio that she needs to make adjustments. Letting the kid hang out down there in the gutter scrappin’ with street punks, what if the creep had a gun? Yukio laments “great,” now Logan of all people wants to put her away for neglect. Pointing her finger at Logan, Amiko angrily tells him that he doesn’t know anything. Yukio takes care of her, not him, so mind your own business! With that, Amiko runs off as Yukio calls out to her to come back. Once she leaves, Yukio tells Logan that she will go talk to her but Logan tells her to stay and deal with the window, he’ll go talk to her.
In a nearby alley, Amiko kicks some trash and looks down at her bloody fist. Walking over to meet her, Logan tells her to let him take a look at her hand. When he sees it, he states that it looks like she’s got some pretty expensive dental work in her knuckles. As he proceeds to pull the teeth out of her fist, Logan tells Amiko that he’s made some mistakes with her. It’s not that he doesn’t want to be around, it’s just his life is very complicated. When her mother died, he swore to her he’d protect her, Amiko, and take care of her like she was his own. He then tells her that she’s with Yukio now because she can provide for her in a way that he can’t.
Amiko apologizes for what she said, it’s just when she gets mad… Logan tells her, pum’kin, that he has the same problem. Amiko replies that Yukio doesn’t make all her choices. She knows what she’s doing and he shouldn’t blame her for what she does. Logan grunts and then says Mrs. Cleaver, Yukio ain’t. He then tells Amiko that he brought her something. When she opens it up, she discovers a stuffed animal – Eddie. Amiko tells him that it’s really, uh, cool. Seeing her disappointment, Logan tells her that he’s got forty thousand yen in gold teeth; does she want to go shopping? A tad disgusted by the bloody teeth, Amiko tells him okay.
Later, back at Yukio’s penthouse, Yukio asks Logan what he’s thinking about as she gives him a hug from behind. Logan tells her Japan, he guesses. Coming there used to help him put away a lot of old regrets in his life. Now he has as much baggage there as anywhere. Yukio tells him that he thinks too much. Amiko is in bed, so why don’t they work on some new, nicer memories for him. Logan tells her maybe later. Truth is, he does have something on his mind, he kinda had an ugly run-in with the Silver Samurai. When Yukio asks him when and where, Logan tells her at the Yashida compound. Yukio replies Mariko’s grave, of course.
While Yukio gets dressed, Logan tells her that something’s goin’ down. The place was deserted, Kenuichio was pretty drunk, acting pretty weird. He said something about being a puppet. He’s tough, he’s never seen him afraid. Yukio asks him why he cares. What has Kenuichio ever done except bring trouble for him and his true love? She adds that you don’t become one of Japan’s biggest crime lords by being a stand-up guy. Logan tells her that he knows, he’s fought against him but he’s also fought alongside him too. He’s not evil, just screwed up. Yukio exclaims that the Silver Samurai has never done anything for anyone unless it benefited himself. He’s made his bed, let him lie in it. Logan replies that’s what he told him, but…
Yukio asks but what? Why get involved? Does he hope to find Matsuo behind the Samurai’s troubles? Finally get revenge for Mariko’s murder? Blood begets blood, he should know. His only obligations there are to Amiko and her, not to the Samurai or to ghosts. Logan asks what if he did find Matsuo, let bygones be bygones? If it was her, she’d…
Just then, Logan stops mid-sentence when a banging is heard at the door. Turning around, Logan and Yukio see the Silver Samurai standing before them in his battle armor. Wielding his sword he tells Logan that he is sorry and collapses before them. Checking the door, Logan asks Harada if he was followed. Harada tells him no, he was careful. Looking at Harada, Yukio points out that his wound isn’t very deep, his armor stopped most of it and tells him that he’s a wimp. Harada then weakly tells them that he had nowhere else to go. Yukio informs him not to worry; Logan was dying to see him.
As he is being bandaged up by Yukio, Harada tells Logan that the man who had him attacked was Haan Kaishek – the new leader of the oldest and most powerful clan ever to come out of Mongolia. The Kaishek’s criminal dominion extends throughout Asia, Eastern Europe and now, thanks to him, Japan. Shingen defended Clan Yashida’s territories from Haan’s father for years, he proved to be much easier to overthrow. Haan spared him so he could help ease in his control of the Clan’s interests. The idea of having Lord Shingen’s mutant son for a henchman amused him.
Logan asks why Haan wants his hide now. Harada informs him that a Japanese industrialist had refused Haan’s offer of partnership and he was ordered to kill his young son. He could not do it. Yukio points out that that resilient moral fiber of his is what’s made him the man he is today. Harada shoots back that she’s spilled her share of blood and asks who she is to…
Peering out the window, Logan sniffs the air and tells them to be quiet. Just then, Logan tells Yukio to take Amiko out the back and to get someplace safe. Grabbing his sword, Harada remarks that it can’t be, he wasn’t followed. Popping his claws Logan tells him to shut up. They’ve got men on the roof so get ready to fight like you deserve to live. No sooner does Logan finish his thought, as does a horde of goons crash through the window toting machine-guns and rifles. As Harada and Logan rush their attackers, Logan tells Yukio to get out of there with Amiko. Once they leave, Logan orders Samurai to bum-rush everybody outside.
As they all tumble out the window and then onto the rooftop below them, Haan watches with his associate Otou and asks if he recognizes the small one. At first, Otou says no but then sees the claws. It is the murderer of Lord Shingen, killer of a thousand Hand ninja, the Wolverine. Surprised, Otou asks that Kenuichio allies himself with his father’s murderer? Haan replies that perhaps to the Samurai, mutant blood is thicker than his own – who knows. From personal experience, he knows family matters can be complicated.
When Otou asks if they should wait for more men, Haan tells him no fool, they take them now while they are unaware. He then tells him to finish what he’s started with Shingen’s son, he’ll deal with Wolverine. Gracefully, Haan leaps from his position. Floating down to where the group has landed, Haan opens up fire on Logan, all the while telling the Samurai to say goodbye to his protector. Instinctively, Logan leaps at him but Haan is able to use his skills to kick Logan off of the rooftop.
With Logan out of the way, Haan turns his attention to Kenuichio Harada and while his men hold him captive, Haan informs him that he has failed him. After one of his men give Harada’s sword to Haan, Haan tells Harada that he gave his word that the boy would be dead, he made him look like a fool. Harada defiantly tells him that he’s a warrior, not a killer. Haan replies that his father tried for years to push Shingen out of Japan and couldn’t. He hated him, but he respected no man as much as his father. He looks at him and he feels cheated. As Logan climbs back up the building side undetected, Haan tells Harada that he’s no warrior, he’s an unruly little boy who pretends he’s a man. Proceeding to stab Harada in the chest, he tells him that in his world, insolent children are punished. While he watches him bleed before him, Haan tells him goodbye.
Just then, Logan climbs up the last part of the building and leaps onto the rooftop. Rushing towards Harada he yells at him to get up. Logan then grabs him and leaps off the building with him in tow. With Logan shielding the fall, he gets them down to the street. Observing the goons jump off the building after them, Logan tells Harada to try and hold on, he’s gotta take care of these guys or they’ll get it in the back.
At that moment, a car speeds up and the man inside tells Logan and Harada to get in quickly for Haan’s men will be there any minute. Entering the car, Logan tells the man inside, Gom, nothing funny or he’s dead. Watching the car speed off, Haan holds his arm that was sliced by Logan’s claws and remarks that Gom must be desperate. Inside the car, Harada weakly tells Logan that he can sheath his claws, he knows this man. He then tells Gom that he didn’t think he’d come. Putting her hand on Harada’s chest, Kia tells him to try not to speak.
Gom, a portly platted-haired individual tells Logan that there is nothing to worry about. His friend, Kenuichio asked him for his help and he is there to give him sanctuary from his brother. Logan replies his brother huh and asks him what one Samurai is gonna do for him. Gom states information on Clan Yashida and Haan’s takeover that may help him reclaim his birthright. Logan remarks that it sounds like a family feud. Gom admits that it is and says that he’d be more concerned about those gunshots if he were him. His sister Kia will… Logan declines and tells him that he’s all right. Noticing Logan’s wounds healing, Gom asks that he is him, isn’t he – the unstoppable Wolverine.
Later, at one of Gom’s safe-houses in Japan, Gom tells Logan that Haan is unaware of his home in Japan and that Kenuichio will be quite safe there while he recovers. Logan replies “good,” then he’s outta there. Gom tells him that he was hoping for a few more moments of his time, he has a proposition for him that… Logan immediately cuts him off and tells him no thanks, just show him the way out. Gom replies that he assumed that would be his reaction and then tells him to follow him to his way out.
Inside another room, Gom asks Kia to turn the screen on. Logan tells him he doesn’t need a tour, just… Gom cuts him off and apologizes to him, but he feels that his offer will appear more attractive coming from someone he trusts. Looking at the screen, Logan sees Yukio and Amiko there with guns pointed towards their heads. Upon seeing them, Logan remarks ‘not again.’ Gom informs him that he lost three men to the woman. Luckily, they subdued the child and she became more reasonable.
Yukio tells Logan that they caught them when they were escaping the fight, she tried to… One of Gom’s men yells at her to tell him. Yukio tells Logan that they want him to assassinate Haan Kaishek, if he refuses… Gritting his teeth, Logan asks Gom where the captives are at. Gom proceeds to tell him to stay where he is, they are safe and far away. Safe they will stay as long as he plays his part.
As he tells Logan this, Gom takes the stuffed toy Logan had given Amiko earlier and slices it in two parts. Haan’s Tokyo penthouse is a fortress but with his claws, easily accessible. They will not be prepared for someone like him. Reaching down for the toy, Logan looks at it and then proceeds to lunge at Gom, attempting to shove it down his throat, and asks him where they are. On the screen, Amiko has a knife put to her throat. Seeing that, Logan stops his assault on Gom. Kia then walks up to him, puts her hand on his chest, and asks him to please calm himself. Gom is desperate, they are no match for Haan and his army of men. She asks that he does as he is asked. Slay Haan and she promises that the women will be returned to him alive. Gom proceeds to pull a gun out of his jacket and says good advice.
With that, he shoots Logan directly in the temple. With blood running down his face and the bullet lodged in his forehead, Logan growls at Gom. Undeterred, Gom tells him that he will kill his brother and help him claim his birthright or his women are dead!