In the Past in Japan, Yolyn Kaishek murders his father to gain the first seat and leadership in the Kaishek house, so he could rule over the Kaishek Dominion, which included clan Yashida.

Present in Japan at Clan Yashida's compound, Logan visits the grave of his beloved Mariko Yashida. Logan remembers back when Mariko had begged him to release her from the pain of blowfish toxin poisoning with his claws. Silver Samurai, half-brother to Mariko Yashida and current leader of the clan Yashida, shows up with a wine bottle in one hand and completely drunk. Silver Samurai tells Logan that he considered Mariko to be lucky to have died back then, than to manipulated into a puppet like him. Logan slaps Silver Samurai and tells him that it was he who wasn't there for Mariko when she needed him, then Logan leaves the same way he came.

On a hill just above the Yashida compound, Gom Kaishek and his sister, Kia watch as Logan leaves. The two recognized Logan as Wolverine, the mutant warrior. Kia asks how Gom was going to get Wolverine to help them. Gom tells Kia that all honorable men have weaknesses.

In the City at Yukio's apartment, Logan meets up with Yukio, who watches over Amiko, Logan's adopted daughter. Logan ask to see Amiko, Yukio tells him that Amiko should be on her way home and if they hurry they could meet her half way. As they walk down the street Logan tells Yukio about his latest adventures; suddenly a man crashes through a window from a street side teahouse and lands unconscious on the sidewalk. Amiko stands at the shattered window; Yukio tells Amiko that she isn't going to teach her any more martial art moves until she learns her lesson. Amiko tells Yukio that the guy was drunk and was grabbing her friend. Logan tells Yukio that Amiko shouldn't be allowed to hang out in such a run-down neighborhood. Amiko yells at Logan to mind his own business, since he is never there for her. Amiko runs off, Logan tells Yukio to take care of the window, while he goes to talk to Amiko. Logan finds Amiko in an alley, Amiko is mad at herself for mouthing off to Logan, Logan tells her that he is sorry he hasn't been around. Logan gives Amiko a doll, but she really doesn't like it, so Logan takes Amiko shopping.

Later that evening at Yukio's apartment, Logan stares out the window thinking about who Silver Samurai was drunk and appeared to be afraid of something. Yukio tells Logan that Silver Samurai does nothing but help himself and that Logan's responsibilities in Japan were to herself and Amiko and not the Silver Samurai. Suddenly, Silver Samurai stumbles in and collapses on the floor, with a short sword in his back. Yukio stitches up his wound, while Silver Samurai explains that Haan Kaishek, the leader of the oldest and most powerful clan of Mongolia. Haan spared Silver Samurai's life in exchange, Silver Samurai was supposed to kill the son of a Japanese industrialist who had refused to partner with Haan. Silver Samurai tells them couldn't kill the boy, now Haan want Silver Samurai dead for making him look like a fool. Just then, Logan senses that they are going to be ambushed. Logan tells Yukio to take Amiko and escape, then tells Silver Samurai to fight like he deserves to live. Suddenly armed men crash through Yukio's apartment window, fire their automatic weapons. Logan and Silver Samurai work as a team and push them back out the window and they fall to the street below. Haan and the rest of his men jump down to continue the attack. Haan recognizes Haan open fire with dual pistols at Logan, which blast Logan off the balcony. Haan's men grab Silver Samurai, Haan stabs him in the chest. Logan made his way back up the side of the building, grabs Silver Samurai, leaps off the building and they land in an alley. A limousine pulls up, A man by the name of Gom tells them to get in, so they can escape. Logan and Silver Samurai get in and they drive off. Gom tells Logan that Haan is his brother and he needs his help to reclaim his birthright from his brother.

Later at Gom's secret home in Japan, Doctors tended to the Silver Samurai's room. Gom ask for Logan to help him to kill his brother, Logan refuses to get involved. Gom reveals to Logan that he had kidnapped Yukio and Amiko, and would set them free if Logan would kill his brother, so that he could reclaim his birthright. Logan gets so made he grabs Amiko's stuffed animal from Gom and rams it into his mouth. Kia tells Logan that Gom is desperate and to please help. Gom gets up and shoots Logan in the head, which ricochets off his adamantium skull. Gom demands that Logan kills his brother or he will kill Amiko and Yukio.