In 1945, Wolverine is in a Japanese prison camp just outside Nagasaki. When the atom bomb is dropped, most of the camp staff commits seppuku, but just one, Yashida, runs for his life and is protected by Wolverine shielding him while his healing power allows him to survive the full blast.
Since he was forced to kill Jean, Wolverine has taken a vow of nonviolence and lives as a hermit in the Canadian wilderness. When a hunting team illegally shoots a bear with a poison arrow and forces him to end its agony, he’s driven to go back on that vow and takes revenge on them. The fight is interrupted by Yukio, a mutant who can see when and how people will die, who works for Yashida. She gets Wolverine to come to Japan, saying that the dying Yashida simply wants to thank him in person for the life he’s had since the war.
However, it turns out Yashida’s company has created a way to transfer mutant powers, and he wants Wolverine’s ability for himself, appealing to how he must want to have a normal life and death by now. He’s also received threats against his granddaughter Mariko from the Yakuza, and wants to stay to protect her. Wolverine declines, and as he leaves sees Mariko’s father Shingen slap her, causing her to attempt suicide before Wolverine saves her.
Wolverine wakes up to find Yashida’s doctor breathing a green gas into his face, revealing her as the mutant Viper. Then he sees Yashida has died, leaving Yukio confused that she didn’t see it. The funeral is attacked by Yakuza disguised as priests, and Wolverine’s attempts to fight them off are hampered by his healing being weaker due to Viper. Luckily, a strange archer appears and helps him, letting him get Mariko to safety. The Yakuza attack again on a bullet train, making clear Mariko is their target, and Wolverine takes her to safety in a romantic fantasy hotel.
The next day Mariko takes him to her childhood home at Nagasaki, and reveals the archer is Harada, her childhood boyfriend who she was forbidden to marry, so that she’s now engaged to the Minister of Justice Noburo. Also, Shingen hit her because Yashida had just revealed he would be bypassed in the inheritance, with the entire company going straight to Mariko.
The next day, more Yakuza arrive and take Mariko, with Wolverine only able to capture one who tells them Noburo hired them. Just then Yukio arrives, revealing that she saw a vision of Wolverine’s death, holding his heart in his hand. They confront Noburo, who reveals Shingen was actually behind the hit on Mariko due to the inheritance.
The Yakuza take Mariko back home to Shingen, but at the same time Harada and Viper arrive with a group of ninjas that capture her for themselves. Wolverine and Yukio also come to the house where Wolverine finds a parasite on his heart with Yashida’s medical scanner, and agonizingly cuts himself open to pull it out despite the warning of his death. Shingen attacks Yukio and is about to kill her when Wolverine recovers, and with his healing restored easily beats him. He intends to leave Shingen alive with his guilt, but after one last attack from behind kills him instead.
Wolverine and Yukio follow a message from Harada to Yashida’s childhood home, where Wolverine is ambushed by the ninjas and Harada knocks him out with Viper’s venom. He wakes up locked in a restraint, with a giant version of the family’s ancestral silver samurai armor made of adamantium prepared to cut his claws off. Mariko escapes Harada and frees Wolverine, and Harada switches sides as he only cares about her safety. The Silver Samurai kills him, and then fights Wolverine and ends up cutting off his claws, while Yukio takes on Viper and ultimately hangs her. The Silver Samurai drills into Wolverine’s hands to extract the adamantium, and is revealed to be Yashida, still obsessed with immortality. Mariko stabs him with the severed claws, and Wolverine extends his old bone claws to finish him off.
Mariko asks Wolverine to stay with her, but he insists on going back to America now that he’s started to make his peace with what happened to Jean. Yukio accompanies him, and he simply tells her to send the plane up for now, undecided on where he’ll go from here.
The Stinger: Two years later, Wolverine is approached by Magneto and a fully resurrected Xavier, who warn him about a great danger that will soon arrive, which they’ll all need to work together to stop.
