In 1945, Logan, portrayed by Hugh Jackman, known as the Wolverine (prior to acquiring his Adamantium claws), finds himself imprisoned in a Japanese POW camp located near Nagasaki. As allied bombers approach to launch an attack, a young Japanese officer, Yashida, defies military orders to liberate the allied prisoners. Among those freed is Logan, but he quickly understands that the impending assault is unavoidable. While Yashida declines to take the honorable route of ritual suicide like his fellow officers, tragedy strikes as the atomic bombing of Nagasaki ensues. Logan heroically saves Yashida, shielding him from the devastating blast, which allows Yashida to witness firsthand Logan's extraordinary healing abilities and his immortality.
Fast forward to the present day, Logan now resides as a reclusive hermit in Yukon, haunted by visions of Jean Grey (played by Famke Janssen), stemming from their troubled past, notably from the events of X-Men: The Last Stand. His quiet life is disrupted when Yukio (played by Rila Fukushima), a mutant who possesses the ability to foresee people's deaths, tracks him down on behalf of Yashida, who has since become the CEO of a major technology firm and is approaching the end of his life due to cancer. Yashida wishes to repay Logan for saving him during the war.
Yashida, one of Japan's wealthiest magnates who significantly contributed to the country's post-war recovery, extends a peculiar proposition to Logan: to transfer his healing powers into Yashida's body, potentially granting him a chance at life while freeing Logan from what he considers the curse of immortality. However, Logan refuses this offer and plans to depart Japan the next day. Before he leaves, Yashida alarmingly warns him that Mariko, Yashida's granddaughter portrayed by Tao Okamoto, is in jeopardy. Witnessing a heated argument between Shingen (played by Hiroyuki Sanada), Yashida's son, and Mariko, Logan intervenes just in time to prevent her from taking her own life.
The plot thickens as Shingen is informed by his father that Mariko is to be his successor, a revelation he vehemently opposes. During a tumultuous night, Yashida's doctor, Dr. Green (Svetlana Khodchenkova), injects something into Logan, leaving him confused and disoriented. After Yashida's sudden death during the subsequent funeral service, Shingen demands Logan to leave. Yukio admits she did not foresee Yashida's demise, adding to the intrigue surrounding his death.
As Logan and Mariko navigate their way through Tokyo's chaos, Yakuza gangsters attempt to kidnap her, leading to a daring escape facilitated by a mysterious assassin. Yet, Logan is injured, and surprisingly, his regenerative powers do not heel as expected. Following a fierce conflict aboard a bullet train, the duo seeks refuge in a love hotel, where Logan grows increasingly suspicious of Shingen's intentions. Meanwhile, Harada, Yashida's bodyguard (played by Will Yun Lee), meets with Dr. Green, who warns him about Logan's newfound vulnerability due to a device she implanted within him.
Logan and Mariko's relationship deepens as they journey to Yashida's ancestral home in Nagasaki, yet danger lurks as Mariko is captured by the Yakuza. After intense confrontations revealing a conspiracy involving corrupt Minister Noburo Mori (Brian Tee), who has plotted against Mariko to ensure his own financial gain, Logan faces formidable opposition. The story unfolds with shocking twists as Shingen is poisoned by Dr. Green, and a relentless chase ensues.
As the narrative escalates, Logan discovers the fight for his powers is far from over. He confronts the Silver Samurai, an imposing adversary equipped with a mechanized suit and blade forged from Adamantium. In a climactic battle involving treachery and fierce loyalty, Mariko intervenes in a dramatic turn of events, ultimately forcing Logan to confront his pain and embolden his resolve. With Yashida's true motivations laid bare, Logan is faced with emotional trials, culminating in a heartbreaking farewell to Jean Grey, marking a significant character turning point.
In the aftermath, Mariko ascends as the new CEO of Yashida Corporation while Logan prepares to leave Japan, vowing to explore the unknown alongside Yukio, who pledges to remain by his side. The journey concludes with a tantalizing tease as Logan returns to the United States two years later, only to find himself confronted by familiar faces: Magneto and Professor Xavier, hinting at an impending crisis that threatens the future of the mutant kind.
