Logan returns to the Canadian wilderness a few years after the events of "X-Men: The Last Stand". Haunted and guilt-ridden by Jean Grey's death, Logan again seeks the quiet life, attempting to renounce his life of violence. One night, he notices a mortally wounded grizzly bear. When Logan encounters the bear, he discovers that a poison arrow has been shot into its back, and Logan is forced to kill it to put it out of its misery. Logan later encounters one of the hunters responsible for killing the bear in a bar, and stabs him in the hand with the same arrow, only to be attacked by the hunter and other men in a bar. As he is about to attack them, he is stopped by Yukio, a young Japanese woman with the ability to see into the future. Yukio reveals that she was tracking his whereabouts and takes him to Japan to see the man he saved from the Nagasaki bombing in 1945, Ichiro Yashida, now the head of the Yashida Corporation.
Wolverine meets Yashida, who wants to return the favor and take his immortality away from him and give it to himself, who is dying of cancer. After Wolverine refuses, he meets his son Shingen Yashida and his granddaughter Mariko Yashida - whom he saves from a suicide attempt. That night, while Wolverine dreams of Jean, Viper injects a robotic parasite into his body, affecting his healing ability. When he woke up, he learns that Yashida had passed away. The next morning, Wolverine attends the funeral of Yashida, where he saves Mariko from Yakuza assassins with the help of Kenuichio Harada. Wolverine gets shot multiple times and finds he is not healing as quickly as before.
After getting Mariko to safety, Wolverine follows her onto a bullet train, where he encounters more Yakuza assassins and kills them before they hide in a local motel. He stands guard in the rain while Mariko sleeps, and soon passes out from his injuries after having another hallucination of Jean. He awakens to find Mariko getting the motel owner's grandson, a veterinarian, to stitch him up.
Wolverine and Mariko then hide in Yashida's house in southern Japan, and as they start to fall for each other, Logan reveals moments from his past such as the war and Jean. Yukio then has a vision of Logan dying with blood everywhere and his heart in his hand, not beating. She attempts to warn him but is too late, as Mariko is captured by the Yakuza who, after intimidating him, revealed to be hired by Mariko's fiance - the corrupt Chief of Justice Norubo Mori. After going to his hotel with Yukio, he reveals that Shingen had hired the kidnapping before being thrown off by Wolverine, landing in a pool.
Wolverine and Yukio arrive at Yashida Corporation, where he finds the parasite on his heart. He starts to extract it when Shingen enters, with Yukio defending Wolverine. Wolverine dies in the process, but has his healing ability restored and revives, killing Shingen. Yukio and Wolverine then follow Harada and Viper to the research center to find Mariko, where Wolverine is attacked by Harada and the Yashida family's ninja clan.
He is then placed in a machine created by Viper, where she reveals the plans of extracting his immortality and introduces her associate, the Silver Samurai, who . Mariko escapes from Harada and manages to direct the machine Logan is in into the Silver Samurai's sword strike, breaking it and freeing him. The Silver Samurai, who revealed as Yashida, cuts through Wolverine's claws and drills through his adamantium claws and begins to extract his immortality. Mariko then stabs him as Wolverine's bone claws start to grow back. Yashida takes a final stab from Wolverine and falls to his death. After passing out, Wolverine had one more hallucination of Jean and moves on from her death.
Logan says goodbye to Mariko, now head of the Yashida Corporation, and boards a plane with Yukio, who reminds him that she is still his bodyguard and they depart.
Two years later, Wolverine is at an airport in the USA and is approached by Magneto and Charles Xavier about a new threat to wipe out all mutants.
