Wolverine is back in Tokyo, Japan. He spends some quiet time walking alone down the streets, until deciding to enter a restaurant. There, he meets up with Irashaimase, a waitress he knows from his usual visits there. Suddenly, Logan is surprised by a happy salute from Yukio. They joke about Yukio wearing leather clothes again, though she isn’t exactly “working” at the moment. The waitress asks Logan if he wants his usual beer, but Logan was actually more up for a sake called “Hitori Musume,” which translated means “Only Daughter.” Yukio suspects that Logan has deeper thoughts in ordering that menu.
Logan admits that he was hoping to catch up with his adopted daughter, Amiko, because he wanted to spend some time with her, seeing that Girl’s Day is coming up. But Logan’s a little sad, because Amiko seems to lead her own life now and doesn’t seem to want to spend some time with him. Yukio smiles, explaining to Logan that Amiko is a teenager now and that at least she has outgrown her rebellious phase from a while back. Now, Yukio mentions, Amiko is in a moody, mysterious stage and just wants some attention. Logan feels even sadder hearing that, and thinks that maybe Amiko might have been better off with a real loving Japanese family and not with a thief like Yukio and a mutant like him who comes to visit occasionally.
Yukio corrects Logan, saying that family values in Japan are changing faster in this town than anywhere on Earth, and kids have to struggle to keep up with the rest of the world. But that isn’t a bad thing, Yukio says, since thanks to her and Logan himself, Amiko is better adjusted to life in the now fast-paced modern world. That’s what scares Logan, he jokingly smiles, but he’s okay with it as long as Amiko doesn’t cut her hair and cuts the letter “k” from her name to sound more masculine. Logan draws a letter “k” on a napkin, and smilingly asks “Yukiko” if she agrees with that.
Yukio gets angry hearing that joke, as she thought that she and Logan had agreed long ago to never bring that phase of her life up again. They change the subject and eat some dinner. After it, Logan asks Yukio if she is in some kind of danger, since he came to Japan to spend some time with Amiko, and the first thing Yukio did was arrange a dinner away from her so that they could talk in private. Yukio, ashamed, admits it. She explains that she has been hearing a voice. Yes, singular. And that same, female voice has been around in Yukio’s head for a few days now, repeating the exact same words about some evil twin sisters, an ancient evil and the end of the world. And it also mentioned something about the protector of Japan itself.
And it all began when Yukio came into the possession of a strange necklace. Wolverine recognizes it as a handicraft, intricate carving object from the Muromachi period around 600 years ago. Yukio mentions that she came into the possession of the jewelry when she heard some rumors. She heard about the necklace, which is called the Mark of Mana, which had been floating around for years. Yukio never believed the rumors until word reached her last week that she should check out an old temple just outside of Tokyo. Though Yukio isn’t a big fan of venturing outside of Yukio, the information came from a reliable source from her so she decided to check it out. She grabbed the necklace from the temple and fought her way out beating up some weird Buddhist warrior monks who were protecting it. And that’s when the voice first started.
Wolverine wants to know why Yukio didn’t turn to Japan’s heroes, referring to Sunfire and the Silver Samurai. Yukio says that Logan was the only one she knows who knows something about mystical stuff. And besides, Yukio says, neither Shiro nor Kenuichio would rush to come to the aid of a thief like herself. Yukio begs Logan to help her out. Logan knows that he’s going to regret it, but decides to go for it anyhow.
Some time later, Wolverine has decided to take Yukio to his old friend, Kenichiro, whom he nicknames the Cat. Wolverine has known the guy for years and trusts him completely, and there is no case which involves magic that Ken doesn’t know about. Once inside his temple, they get a warm welcome from the man. They catch up and Ken is glad to see that Logan’s still doing well with the woman. Yukio doesn’t know what to say but Logan calls her just a friend and informs Ken that she’s the reason he’s there. Ken already thought that, and takes his friends to his study, which has lots of books and other rare items installed. Yukio is in paradise!
Ken offers Logan and Yukio to sit down and tell him what the problem’s about. Yukio shows Ken the necklace. Just by seeing it, Ken panics. He recognizes it as the Mark of Mana. Ken gets upset and can’t believe that Logan would actually bring such evil to his sacred place. Logan apologizes, since he didn’t know it was so evil. Ken explains that legend has it that an evil spirit is inside the necklace. It’s a vengeful goddess, who haunts all those who it comes into contact with. Kenichiro doesn’t like this situation at all. But he knows that there exist spells to further contain the spirit, though they might already be to late to do that.
Ken is literally spooked and drops everything he holds. Logan tries to calm him down and is surprised to see his friend in this state, something Logan has never seen before. That’s because Logan never brought an impending doom into his life, Kenichiro explains. Ken takes some charms out of a drawer, and gives Logan the mission to take them and get out of his house. Ken informs Logan that the charms should protect him for now. Logan doesn’t understand what’s going on, but suddenly he hears a noise from outside. He goes to check it out. Suddenly, lots of arrows fly around through the room, and one hits Logan. He quickly takes it out, and isn’t hurt or poisoned -so his attackers aren’t the Hand.
Ken fears that they came for the Mark. And since there’s only one way out of the temple, meaning the front door, they’ll have to defend themselves and fight. So each of them takes out a sword or their claws and stand ready. Weird-looking ninja’s enter the place and are apparently a bit surprised to see someone with claws. The fight goes on for a while, and both Wolverine and Yukio manage to defeat their foes. But Kenichiro gets hit too much, but begs them to protect the necklace. He tries to say something else, but dies.
Logan gets angry and doesn’t understand. He picks up the necklace, and inside his head sees an image of a place filled with fire and two look-a-like girls fighting each other in front of a temple and both wearing the Mark.
Logan drops the necklace and tries to recover. Yukio asks if he’s all right. Wolverine isn’t, but the vision he had told him where to start looking for answers. He tells Yukio to grab the Mark and come with him. Logan’s angry. His friend died because of this, and now there’s going to be hell to pay!