One night in New York, Logan saves a man named Tesshin Asano who was being attacked by members of AIM equipped with cloaking devices and metal destroying weaponry. Asano tells Wolverine about the whereabouts of his missing love, Mariko Yashida, and the crime organization Kuzuryu, the leader of which is Mariko's father, Shingen. Mariko is allegedly arranged to be married to a man named Hideki Kurohagi in order to expand his operations. In order to find Mariko, who was kidnapped from New York a year ago, Logan flies to Tokyo and infiltrates the Yashida household, but is detected by Shingen. After his henchmen are defeated, Shingen challenges Logan to a bokken fight. Logan barely manages to withstand Shingen's swordsman skills, but is shot with a drugged dart by Hideki, before going into a rage and bringing out his claws.

After Hideki shoots a drug in Logan to slow his healing factor, he loses the fight and Shingen's henchmen take his body to a railroad track. Asano follows the men to save Logan only to see he was gone. Logan awakes in an apartment treated by an assassin named Yukio. Logan goes to Asano's office to give him evidence, but finds him stabbed in the heart with a thin blade. The police arrive on the scene to see Logan and Yukio standing near the body of Asano. The duo escape and slaughter Yakuza trying to ambush them. Outside, a mutant name Kikyo Mikage, who has similar powers to Wolverine's, appears on the roof ready to fight him.

As Logan and Kikyo fought, more police arrive to see the two destroy the area, which Kikyo escapes and Logan retreats. Mariko sits silently as her father practices his kendo, but smiles when overhearing Hideki tell her father Logan is still alive. Yukio and Logan search for a lead and find Yashida clan members unloading a secret cargo from a docked ship. The police are in wait for the cargo to be dropped off and arrest the clan members. Logan then throws Molotov Cocktails and sets the vessel on fire, and then intercepts Hideki before he can escape. The cargo is revealed to be Omega Red who has come to Japan for revenge on Logan and grabs him with his long metal tendrils.

Logan's fight with Omega Red takes its toll on him regardless of his healing factor. In a flashback of one of Logan's black ops missions, he was to infiltrate and steal a power source for a Soviet era weapon, which drains the life force of any weapon it touches with its carbonadium tendrils, which are a KGB experimental counterpart to adamantium. As Logan steals the power source, he runs into Omega Red and leaves him to die in a cave in the snow. In present day, Omega Red blames Wolverine for his pain because without the synthesizer, his body was vulnerable to biological attack. To buy time and escape, Logan throws a flammable container at Omega Red which explodes and destroys the dock. While resting in a vacant apartment, Wolverine senses an assassin. The assassin is really a decoy for Omega Red, who reappears with a severely burnt face, and pins Logan to the wall and knocks Yukio back.

Logan beaks Omega Red's hold on him and their fight drags onto the street. Elsewhere, Shingen takes Mariko to Madripoor in a private jet. Yukio throws her ring blade at Omega Red and Logan uses it to sever Omega Red's right arm and slices the box on his chest, defeating him. Logan learns that Mariko is to leave for Madripoor soon so he pulls out a beacon with the X-Men insignia. As Logan and Yukio head to the Yashida house, A.I.M. takes Omega Red, still alive, back to a secret base in a stealth ship. At the Yashida household, Kikyo waits for Logan to finish their fight from earlier. As police storm the house with a search warrant, Logan and Kikyo take their fight to the top of a tower. At the house after finding nobody home, an autopsy report is sent to the detectives who worked with Asano, with the results saying that a hair was found in Asano's teeth with the DNA proving Logan's innocence. At the top of the tower, Omega Red wants to fight Logan with his new cybernetic right arm, only for Logan to win by destroying the box on Omega Red's chest. The fight weakens Wolverine, and Kikyo says he will not fight Logan in his current state as it goes against his code of honor. After the fight, the X-Men's airship the Blackbird decloaks with Cyclops piloting in response to take them to Madripoor.

Logan introduces Yukio to Cyclops as they make their way to Madripoor. After dropping off the duo, Cyclops heads home. Yukio and Wolverine are then ambushed by pirates and easily dispatch them. Logan goes on ahead leaving Yukio to handle the pirates alone. At night as Logan reaches another shoreline, vagrants jump him only to be shocked at his power. Two bikers chain Wolverine's leg from a motorcycle and drive him to a post and hang him upside-down. Not showing any concern, Logan cuts himself down and takes the motorbike. As soon as a mob of people come after him, a young girl throws knives at the men, killing them. The girl states that she saved Logan in hopes that he could work with her, but he turns her down. After she says she works with others who try and stop Kurohagi, Logan wants answers. She questions his reasons for wanting to kill Kurohagi, but he will not answer. She tells Logan where to find Kurohagi, in the most brightly lit tower on the island called Dragon Palace. Meanwhile, blindfolded Yashida cuts candles off a table and lines them up along the flat side of his katana, entertaining guests to his daughter's wedding, and throws them on to pillars of a gold statue of Kurohagi's father. As Kurohagi thanks Yashida for the show, a subordinate tells him that Logan is on the island. Despite Min's warnings, Logan still chooses to go. Knowing now Wolverine is on the island, Kurohagi sends the behemoth Vadhaka to take him which sends tremors through the island. The creature lands in front of Logan stating he will not pass.

When Vadhaka attacks Logan and Min, she tells him the statue belongs to Hideki Kurohagi and is the spirit of Madripoor, but the statue can't move unless the seal was removed. As they run, a crazed mob attacks and Logan directs them to a dead end alley way. Logan tries to protect Min, only for a rival group to attack the ones that chased the two. As soon as they flee the mobs, the statue intercepts them with Logan using his unbreakable skeleton to shield Min from Vadhaka's fists. Logan brings out his claws on the wall so Min has space to escape as he gets pummeled, but is captured by the locals. Yukio then saves Min with her ring blade, then Wolverine resumes fighting. Vadhaka then kicks Logan into the building behind him and Logan makes his way to fight the former in a more spacious area. Yukio pours quick-drying cement on Vadhaka to give Logan a chance to get out. Thinking that Vadhaka is encased in the cement, Logan and Yukio make their way only for the statue to easily break free and attack. Min arrives and uses a steam pipe that burns her hands to distract Vadhaka long enough for Logan escape far from the battle scene, but with Yukio hidden under debris. In the sewer as Logan tries to leave Min, a group approaches that Min says are her friends. As Logan tries to leave, he catches a knife-tip cane and throws it back. Logan meets Master Koh who offers a trade with Logan. Meanwhile, Kikyo arrives on the island killing four locals who attack him as he searches for Logan. Koh informs Logan that the wedding will be earlier then first thought, and he needs Logan to help win a guerrilla war to retake Madripoor. Elsewhere it turns out that Vadhaka is an A.I.M. robot. Koh tells the story of how Kurohagi Sr. gained control of the island and how he is Yukio's grandfather on her father's side, but Logan doesn't piece the latter fact together. When the cameras in Koh's base are hijacked, Hideki puts Yukio on screen saying he'll kill her if Logan doesn't surrender. When Koh hears this, he tells Logan that Yukio is his granddaughter.

As a broadcast of Yukio's location is sent to Koh's base, Logan says he will go save her first rather than let her die to get his revenge, with Koh believing the opposite. Making a deal that Logan will distract Kurohagi when he arrives at Dragon Palace so that he and his men can attack, Koh gives Logan a map with a direct route to Dragon Palace named "Hell Road" due to its history of people going in but dying when they are caught. As the grunts watching Yukio play with her weapon, they reveal that they have automated-military grade weaponry guarding the bunker. When the men go to sleep, Yukio frees herself with her weapon being on the wall, but is tranquilized when Kurohagi checks on the men. The one in charge of guarding Yuiko is killed by a dart of a more potent and lethal version of the one used on Logan at the Yashida home. Logan easily disables this system and uses the ammo to break through the door of the bunker and unties Yukio. Logan picks up a tranq-dart, and takes it with him as the duo head for Hell Road.

Logan and Yukio enter Hell Road and Yukio explains the history of the road as it was built. The only person to make to the top was Juo Kurohagi, Hideki's father. Later, they encounter traps and push through them barely managing to get by. They proceed by foot when the motorcycle they were on is destroyed by spears. As they make their way passed trap on top of trap, they fall down a trapdoor with spears at the bottom. Meanwhile, Koh takes his men through a secret underground path he didn't inform Logan about. Upon hearing that his granddaughter Yukio is with Logan, he still proceeds with his plan to take down Kurohagi. As they were falling, Logan used his claws to grasp the wall and hold on to Yukio. Locals who saw them still alive attempt to close the door, but Yukio manages to get out and dispatch them. Logan then makes his way out and both of them continue to run into more traps and locals. Meanwhile, Vadhaka returns to an angry Hideki who knows Logan still isn't dead, and that Logan is on his way on Hell Road, so he calls for the ceremony to start immediately. As more traps are activated, Logan and Yukio still manage to get through with local enemies get killed in the process. With one trap by one group of vandals taken out, the power balance shifts, causing unrest between criminal groups. As the duo near the Dragon Palace, they are stuck in the ground as it is liquified. Koh and his men emerge from the passage to find the road as Logan had left it as he passed. Frustrated, Logan goes Wolverine and escapes the trap he, with Yukio, are in and takes down the enemies who're trying to kill them. Koh meets up with Logan and has his men handle the obstacles to let him through. When they finally make it to the top, they run into Kikyo.

Logan tells Kikyo he doesn't have time for a fight, and is let to pass by Kikyo who won't fight a weakened opponent. Once Logan makes his way, Hideki Kurohagi announces himself and Logan throws the dart at him. The dart is stopped when it impacts a force field around Kurohagi. He remarks that Kikyo was hired to kill Logan, but with another assassin on the payroll, he is abstaining from the job. Hideki unleashes an upgraded version of Vadhaka on Logan leading to a fight between the two killing machines. As Logan is taking a beating from a more powerful Vadhaka, he uses all his strength to get out a being crushed by Vadhaka's foot. But with all his effort Logan is still losing and is taking a severe attack by Vadhaka. When Vadhaka rams into Logan, the wall around them collapses. Koh and the others meet with Yukio and an angry Kurohagi calls for his robot, Vadhaka. As Kurohagi orders his men to fire on the intruders, Kikyo arrives and disarms them stating that it was dishonorable and he couldn't abide it. Logan escapes the rubble and heals his wounds to proceed fighting, but as he does, so does Vadhaka. Vadhaka moves towards Logan, and smacks Min out of his way. As he is fighting, Kikyo helps even the odds. Yukio tries to keep Min alive, but dies in her arms saying that Kurohagi must be stopped. Enraged, Kikyo uses his WindBlade attack, with no effect. Logan tries to think of a weak point on Vadhaka, Kikyo in agreement draws a second sword from his other arm to use. Logan grabs a spear previously shot, and impales the head of Vadhaka.