Logan awakens. He's in bed with Jean Grey (Famke Janssen), and she asks him what dream it was this time. "Nagasaki" he responds. Logan has bad dreams every night, it seems. The two cuddle, and Logan professes his undying love for her, and then gasps; his claws are embedded in her chest. Fresh blood is pouring out of her stomach. Logan screams, in horror, and awakens from his dream-within-a-dream in a cave in the Yukon.
Present day. Since the end of X-Men: Last Stand Logan has lived a nomadic, homeless, lifestyle. It appears that he lives in the woods like a wild animal, and hasn't bathed or shaved in a while. He lives in a small cave with only the basic of necessities: empty whiskey bottles and an old radio which is losing battery power. Logan dresses and exits the cave, walking through the wilderness to the nearest town. Along the way he crosses paths with a mammoth grizzly bear who, for all appearances, is friendly with Logan. Logan comes to the general store, buys some batteries, and watches as a small group of drunk hunters prepares to go up into the mountains. They're green; one of the hunters nearly shoots his foot off as he goofs around with his hunting rifle. Logan is annoyed.
Logan returns to his cave and sleeps. Cries of agony ring out and he goes to investigate -- he finds the hunters' campsite, which looks destroyed, and evidence of a bear attack. He follows bear prints in the fresh mud and comes upon the same bear from before, with an arrow sticking out of its back. The grizzly is still alive, and in pain. The bear looks to Logan with tear-filled eyes and Logan is forced to put it out of its misery.
Logan plucks the arrow from its hide and sniffs the tip; it's coated in poison. He stalks into to the town and walks into the local bar (observed by a slight young red haired Japanese woman), where he finds the survivor from the group of hunters recounting the attack. The grizzly killed his companions, he was lucky to escape with his life. Logan, angry at the hunter, asks who shot the bear with illegal poisoned arrows -- because the poison was too low of a dose, the bear went on a rampage instead of dropping dead. The hunter denies using poison-tipped arrows, but Logan continues his accusations. Logan drives a knife through the leader's hand pinning it to a table, explaining that the arrow was the one he pulled from the bear's back; if it was not poisoned, then the hunter has nothing to worry about.
The Hunters friends square off about to attack Logan who is prepared to fight them all, when he is persuaded by Yukio (Rila Fukushima): a young, red-haired Japanese woman carrying a samurai sword. She teases the hunters, and shows them her sword, explaining that it is hundreds of years old and is called "Danzan", "The Separator", because its purpose is to separate heads and limbs from bodies. She slices the sword through the air, nearly killing the other hunters in the process, frightening them all, and leaves. Logan leaves with her and climbs into her rental car. Logan asks who she is and why she's been looking for him. She explains that she has been sent by Yashida, whose elderly body is being ravaged by cancer. Yashida wishes to speak with Logan before he dies, and thank him for saving his life 70 years earlier. Logan is reluctant to go to Tokyo, but can't ignore this personal obligation.
Logan and Yukio fly to Tokyo and arrive at Yashida's palatial residence. Logan is turned away by Yashida's American oncologist (Svetlana Khodchenkova) and by Yashida's grieving granddaughter Mariko (Tao Okamoto). They insist that Logan's caveman-like state could prove infectious to the elderly, dying Yashida. Logan is unwillingly thrown into a bathtub and cleaned and shaved until he is less offensive and more presentable. Logan is finally allowed to speak to the elderly Yashida (Hal Yamanouchi), who presents Logan with the same sword he bestowed to him 70 years earlier. Yashida has summoned Logan because he believes his cutting-edge company has the technology to present him with a unique opportunity: They can make Logan mortal, and will transfer Logan's life-giving mutation into his own body. Logan is upset by Yashida's request and argues that no one should want his power. As he begs Yukio to fly him home he observes as Shingen (Hiroyuki Sanada), Yashida's son and Mariko's father, coldly and angrily slaps his distraught daughter. Heartbroken, Mariko aims to throw herself off the nearest cliff, but is saved by Logan. This angers Shingen. Yukio persuades Logan to stick around for another day or two, and finds a room for him to stay in.
As he sleeps, Logan dreams of Jean who climbs into bed with him and kisses him. As the dream ends, Jean becomes Yashida's oncologist. Her snake-like tongue presses deep into Logan's throat and deposits something causing a green vapor to flow from his mouth. He struggles and is knocked out. Logan awakens, having heard a commotion outside his room and exits to find paramedics running through the estate. Seconds later, Yashida's dead body is carted to the entrance. Mariko cries and Shingen hurriedly prepares the funeral.
Days later, Yashida's funeral is held in the center of Tokyo. Logan arrives, with Yukio, and shakily makes his way through the funeral procession. Shingen is especially disgusted with Logan and tells him to go home. Logan and Yukio enter the funeral and stand at the back of the crowd. The ceremony is watched by a lone archer, who quietly whispers to the spirit of Yashida that he will protect Mariko. Mariko is ushered up to the front of the funeral by a pair of traditionally-dressed priests. Logan notices that the priest's arms are heavily tattooed with what are certainly Yakuza markings. Logan bursts through the crowd, angering Shingen, Mariko, and Mariko's distant fiance Noburo (Brian Tee). He spots a gun-shaped bulge under one of the priests' robes and within seconds guns are drawn and Logan is shot in the chest. Logan experiences devastating pain, for the first time in his life. All the priests shed their robes, revealing Yakuza tattoos and clothing. The Yakuza grab Mariko and flee the funeral. Logan chases after them. He's shot multiple times, and struggles greatly to regain his stamina, his healing ability greatly impaired. Arrows come soaring into the funeral, laying-out dozens of Yakuza members. The archer, Harada (Will Yun Lee), takes out many of the Yakuza and chases after Logan and Mariko as they flee the funeral temple.
Logan takes Mariko deep into the city whilst being chased by the Yakuza. Mariko tries to dismiss Logan from accompanying her, but Logan follows and they board a bullet train and Logan pleads for understanding of what just happened. Mariko explains that in three days time, her grandfather's will is to be announced, which will name her (not her father) as the new head of the Yashida corporation. The Yakuza are desperate to kidnap her because it will mean a huge ransom. Logan disappears into the train's bathroom and examines the wounds on his chest; they aren't healing. He shakily exits the bathroom and is met by four Yakuza soldiers who shoot and stab him. Logan retaliates, killing two of the men and ripping a hole in the side of the train. The remaining soldiers are sucked-out onto the side of the train, along with Logan, and the three battle one-another at bullet train speed. Logan defeats the Yakuza and returns to his seat in the train. He asks where Mariko is headed. Her family has a home at "the end of the line". Logan infers that if there were Yakuza on the train, there are sure to be some waiting for them at their destination. Mariko agrees and the two exit the train well-ahead of their destination. The pair walk through the city, in search of a safe place that Mariko is familiar with, but Logan stops her, and explains that they need to find a place to stay where nobody will look for her. Logan finds a seedy-looking hotel and drags Mariko inside. It's a "love-hotel", a pay-by-the-hour establishment. Logan thinks it's perfect, because it's the last place the Yakuza would look for them. They pick a "Mars-themed" room and hurry upstairs. While Mariko sleeps, Logan stands watch on the balcony. He dreams of Jean, and passes-out. Mariko awakens and runs to his aid. Logan awakens in a veterinarian's office. The son of the hotel's manager is stitching-up Logan's wounds. He nervously backs away from Logan as he stirs, and gestures to the fresh slashes on his face and arms, all caused by Logan. Logan is stitched-up and in better form than he was the night before, but he's still far from immortal.
The oncologist sneaks her way through a seedy back-alley. Her blonde hair draws cat-calls from middle-aged perverts who expect her to be a prostitute. She takes one by the collar and spits green acid in his face, blinding him. She continues through the alley and finds Harada, impatiently waiting for her. She's two hours late and he's angry. She demands to know where Mariko and Logan are. Harada's men are still searching, but Mariko hasn't appeared in any of her usual spots. The woman, a mutant who now identifies herself as 'Viper', tells him that they have less than three days to find her.
The following morning, Yukio calls Mariko and pleads to know where she and Logan are hiding. Mariko refuses to say, despite her closeness to Yukio, but promises that Logan is being good and is caring for her. Mariko and Logan make their way to Yashida's long-forgotten home, in Nagasaki. She doesn't expect anyone to follow them there, because the house is old and in disrepair. They buy groceries and Mariko cooks for Logan. Mariko explains that her engagement to Harada is an Arranged Marriage, that for powerful and political reasons she must go through with the marriage. She also explains about the solitary Archer who she grew up with and has wanted to marry since she was 12. She asks him who Jean is, as Logan tends to repeat that name in his sleep. Logan explains the relationship he had for and with Jean, how he loved her and why he killed her.
They go for a walk, and Logan sees something familiar in the distance: the location of the prison camp, and the well in which he saved Yashida, which has long since been capped. Logan helps some locals chop wood, and begins to shed his gruff exterior; this appeals to Mariko. The two return home and eventually make love. The following morning, Logan wakes and can't find Mariko anywhere. He hears her screaming outside. The Yakuza have found them and kidnapped Mariko. Mariko is thrown into their car and Logan runs after them. One of the soldiers shoots Logan, slowing him down, but Logan manages to pull him from the vehicle. He presses the man to the ground and tortures information of Mariko's whereabouts out of him.
Yukio arrives, having followed the Yakuza to Nagasaki, and the pair of them go after the only lead they have: Noburo, Mariko's fiancé. Yukio explains to Logan that she has a gift of second sight or the ability to see death, and that she has seen Logan die with his own heart in his hand. Logan tells here than many have tried to kill him before and that hes still around. They find Noburo in his apartment with a pair of western prostitutes. Logan threatens Noburo, who admits that he and Shingen had an agreement to kill Mariko, and that Shingen has Mariko. Logan throws Noburo off a balcony and into a swimming pool. Yuriko and Logan head back to Tokyo.
Mariko arrives at the Yashida estate, where her father is waiting for her. Shingen explains that he has worked his entire life to take over the Yashida corporation once the elderly Yashida dies. When he discovered that Mariko, and not Shingen, would be inheriting the corporation, he conspired with the Yakuza, by way of her fiancé Noburo, to have her killed before the will was read. Had Logan not intervened on the night of her grandfather's death, and allowed Mariko to jump to her death, Shingen would have inherited the company immediately. Shingen, along with his small army of Yakuza, will now find a way to have Mariko killed while keeping his own hands clean.
Suddenly, black-suited ninjas descend upon the compound and secretly dispatch with the Yakuza. The ninjas are led by Harada and Viper. Shingen is cornered by the ninjas and Viper explains to Shingen that there are greater forces at work than Shingen and the Yakuza. She spits in his face, severely disfiguring it, and tosses Shingen into a pool. Harada, Viper, and Harada's men take Mariko and disappear.
Logan and Yukio arrive and find evidence of the massacre. They make their way into Yashida's private room, filled with high tech medical equipment and x-ray scanners. Logan climbs into Yashida's MRI machine and guides the x-ray over his body and discovers, shockingly, a metallic parasite attached to his heart, implanted by Viper days earlier. The device has impaired his healing ability. Logan, against Yukio's pleas, cuts open his chest and reaches for his heart. Shingen, who had survived Viper's acidic attack, appears dressed in traditional samurai armor. He seeks to kill Logan, and swings his sword at him. Yukio saves Logan, and battles Shingen while Logan reaches further into his chest. Ultimately Logan manages to grab, extract and destroy the robotic parasite, but loses consciousness. He lays on Yashida's bed, with a giant open wound on his abdomen. Shingen bests Yukio, knocking her sword away from her, and aims to cut her in two when Logan's clawed hand appears, blocking the blow. Logan immediately heals, gets to his feet and goes after Shingen. Shingen skewers Logan's body with multiple swords, but is unable to kill him. Logan gets within arm's reach of Shingen, but decides to let him live, arguing that he should live knowing that he tried to kill his own daughter. As he walks away Shingen runs after him, running his sword through him. Logan stabs Shingen through the throat, killing him instantly. Logan returns to Yashida's room where Yukio has found Mariko's whereabouts -- a Yashida facility built in the village where Yashida grew up. She also discovers strange robotic designs strewn about the room. Logan takes a Yakuza motorcycle parked out front and heads to the Yashida facility.
The facility is high in the mountains. Logan drives into the village and watches as dozens of locals citizens flee to their homes. Seconds later Harada appears, and tells Logan to leave. Logan refuses, so Harada slashes at him. Harada watches in disbelief as Logan's fresh wound heals. Harada orders his ninja-clad men to kill Logan. All at once, arrows attached to ropes come streaming-in from the adjacent rooftops, and within seconds Logan is impaled dozens of times. Harada, having dipped the heads of his arrows into Viper's venom, launches them at Logan, weakening him considerably. Logan finally passes out.
Logan awakens inside of the facility, strapped into a stock, forcing his hands forward & away from his body. He can't move. Viper appears, and congratulates Logan on removing her parasite. Logan hears Mariko screaming his name, and sees a massive, metallic mechanical samurai sitting to his left. To his shock, the mech gets to its feet and walks over to Logan. Viper explains that Yashida had been stock-piling adamantium in recent years, having been obsessed by Wolverine's adamantium skeleton. He built this suit of armor out of the material, and with it, Wolverine can be killed. She angers Logan and goads him into extending his claws. As soon as he does so, constraints are clasped onto his hands, preventing him from retracting the claws. Wolverine watches, in horror, as the giant, mechanical, adamantium samurai approaches him and draws an 8-foot long flaming sword. It positions itself to cut off his claws. Mariko struggles with Harada and stabs him. She runs to Logan's side and distracts the Samurai who slashes Logan's restraints open, allowing him to escape. Yukio, who had followed Logan, arrives at the back door of the facility and sneaks inside. She battles Viper while Logan deflects blows from the much larger and stronger Samurai. The Samurai gets the upper-hand on Wolverine and cuts one of hand's claws off, revealing bone underneath the adamantium. Logan battles the Samurai one-handed, wrestles its massive sword away from it and slashes the Samurai's helmet off. The out of control mechanical samurai slashes-open the side of the facility, and pushes Logan out through the hole. Logan dangles hundreds of feet over the ground and hastily climbs back into the facility.
Meanwhile Yuriko is battling Viper, losing when Harada seeing that his actions have been a dishonor makes one last effort to redeem himself and kills Viper and himself.
Suddenly the samurai's sword comes swooping over his head, cutting his other hand's claws clean off, and the pilot of the mechanical samurai is revealed to be Yashida, the old man thought dead. Yashida explains that his life's goal since meeting Logan was to prolong his life, at whatever cost. When Logan refused to go through with the procedure at his estate, he faked his death with the assistance of Viper and kidnapped Mariko, knowing that it would lead Logan to him. Yashida (in the samurai suit) grabs Logan's wrists and six drills come out of the suit's forearms. The needles drill into Logan's exposed bone-claws, straight into the marrow. Within seconds, Logan begins to grow old and Yashida, by way of the interconnected suit, becomes the young Yashida again. Yashida laughs, as he siphons the life from Logan. Mariko has freed herself from Harada and sees and hears her Grandfather's plan. Suddenly one of Logan's separated claws comes flying through the air and lands in Yashida's skull. Mariko, confronts her grandfather and stabs Yashida in the head, again. Logan is freed from the suit's drills, his life returns to his eyes, and Logan instantly grows back his bone claws. Logan stabs Yashida, and pushes Yashida, and the suit, out of the facility and it crashes on the rocks below.
Yukio, who had survived her encounter with the Viper, joins Logan on an airport runway. The biggest news of the day is that Mariko Yashida has inherited her grandfather's corporation. Mariko kisses Logan on the runway and hints that he should come back to see her soon, but the two agree that they have separate paths to follow. Logan boards the plane and Yukio follows. She gleefully tells Logan to consider her his bodyguard, asks Logan where he would like to go and Logan gives her an indefinite response, but he's happy that she's with him.
Two years later, Logan (minus Yukio) is walking into and Airport Security checkpoint and asks for the pat down. An overhead TV shows a commercial for 'Trask Industries', and Logan pays little attention to it. Suddenly the coins, watches, and pens in the X-ray machine begin to float. Logan, aware of this magnetic anomaly, immediately ejects his bone claws and spins around to see Magneto (Ian McKellan) behind him. Magneto freezes Logan in place, and urges Logan to lower his defenses. He tells Logan that his mission is a peaceful one, and that he hasn't come alone. Logan turns away from Magneto and watches as everybody surrounding them both freezes in place. A wheelchair silently weaves through the sea of frozen bodies, and in its seat is Charles Xavier (Patrick Stewart). Logan is speechless at seeing Xavier alive. Magneto and Xavier explain they need Logan to save all of mutant-kind