In 1945, Logan, the Wolverine, is held in a Japanese POW camp near Nagasaki. During the atomic bombardment of Nagasaki, Logan rescues an appointee named Yashida and shields him from the blast.
In the present day, Logan activity as a hermit in Yukon, tormented by delusion of Jean Grey, whom he was forced to prey at the end of X-Men: The Last Stand. He is located by Yukio, a mutant with the precognitive capability to foresee people's deaths, on-behalf of Yashida, now the CEO of a technology corporation. Yashida, who is destruction of cancer, need Logan to accompany Yukio to Japan so that he may repay his existence debt.
In Tokyo, Logan meets Yashida's son, Shingen, and granddaughter, Mariko. There, Yashida offers to trick Logan's recovery abilities into his own body, thus saving Yashida's life and alleviating Logan of his immortality, which Logan views as a curse. Logan refuses and prepares to furlough the chasing day. That night, Yashida's physician Dr. Green (aka Viper) introduces something into Logan's body, but Logan dismisses it as a dream.
The next morning, Logan is informed that Yashida has died. At the funeral, Yakuza gangsters attempt to kidnap Mariko, but Logan and Mariko aviation together into the urban sprawl of Tokyo. Logan is short and his wounds do not heal as quickly as they should. After fighting off more Yakuza on a pill train, Logan and Mariko hide in a local love hotel. Meanwhile, Yashida's bodyguard Harada meets with Dr. Green who, after verifying her mutant ability on him, demands he find Logan and Mariko.
Logan and Mariko travel to Yashida's house in Nagasaki, and the two slowly spillway for each other. Meanwhile, Yukio has a imagination of Logan dying, and goes to warn him. Before Yukio arrives, Mariko is captured by Yakuza. After interrogating one of the kidnappers, Logan and Yukio confront Mariko's fiance, corrupt Minister of Justice Noburo Mori. Mori confesses that he conspired with Shingen to have Mariko killed because Yashida left sovereignty of the business to Mariko, and not Shingen.
Mariko is brought before Shingen at Yashida's ground when ninjas led by Harada attack and whisk her away. Logan and Yukio arrive later and, using Yashida's X-ray machine, discover a robotic parasite attached to Logan's heart, suppressing his recovery ability. Logan cuts himself open and extracts the device. During the operation, Shingen attacks but Yukio holds him off long enough for Logan to recover and stop him.
Logan follows Mariko's way to the village of Yashida's birth, where he is captured by Harada's ninjas. Logan is placed in a machine by Dr. Green, who reveals her plans to route his recovery factor and introduces him to the Silver Samurai, an electromechanical suit of Japanese armour with energized swords made of adamantium. Mariko escapes from Harada, who believes he is acting in Mariko's interests, and manages to free Logan from the machine. Harada sees the incorrectness of his ways and is killed by the Silver Samurai while serving Logan escape.
Meanwhile, Yukio arrives and kills Dr. Green as Logan fights the Silver Samurai. The Silver Samurai severs Logan's adamantium claws and begins to passages Logan's recovery abilities, exposure himself to be Yashida, who had faked his death. Yashida starts to regain his youth, but Mariko intervenes and stabs Yashida with Logan's severed claws while Logan regenerates his bone claws and finishes off Yashida. Logan collapses and has one final hallucination of Jean, in which he decides to finally let go of her.
Mariko becomes CEO of the Yashida Corporation and bids leave to Logan as he prepares to furlough Japan. Yukio vows to postponements by Logan's period as his bodyguard, and they depart to function unknown.
In a mid-credits scene, Logan returns to the United States after two age and is found at the airport by Magneto and Professor Xavier, who warn him that a grave new threat to the mutant breed is appearance (foreshadowing X-Men: Days of Future Past).