In 1845, a young boy named James Howlett, who is often unwell, witnesses the tragic murder of his father by the groundskeeper, Thomas Logan. This traumatic event triggers James's latent mutation, causing bone claws to emerge from his hands, leading him to instinctively kill Thomas, who, in his final moments, reveals that he is actually James' biological father. James's mother is horrified by this revelation and his mutation, resulting in him fleeing into the woods alongside Victor Creed, the son of Thomas Logan and James' half-brother, portrayed by Liev Schreiber.
Together, they become soldiers over the next century, partaking in various wars, including the Civil War and both World Wars. James, who goes on to adopt the name Logan, possesses remarkable regenerative abilities that allow him to survive numerous injuries. However, he becomes increasingly aware that Victor finds pleasure in chaos and violence.
The story picks up in 1973 when Victor goes too far, attempting to assault a woman in their village and subsequently killing a senior officer. James, played by Hugh Jackman, intervenes, leading both brothers to be sentenced to a firing squad, though they manage to survive. They attract the interest of Major William Stryker (Danny Huston) who recruits them into Team X, a covert group of mutants which includes marksman Agent Zero (Daniel Henney), swordsman Wade Wilson, teleporter John Wraith, and others.
Their mission takes them to Nigeria, where Stryker's quest for a meteorite piece of Adamantium leads to morally questionable orders, including the massacre of innocent villagers. Disturbed by these actions, Logan decides to leave the team.
Years later, Logan lives a quiet life in Canada with his girlfriend, Kayla Silverfox. However, their peace is shattered when Stryker informs Logan that members of Team X are being killed, with Victor being the one behind it. After a tragic confrontation that results in Kayla's death, Logan's path becomes one of vengeance against Victor, who has become increasingly unhinged.
In a desperate bid for power, Stryker offers Logan a way to obtain the upper hand: a procedure that will bond his skeleton with Adamantium, making him nearly indestructible. Before undergoing the operation, he asks for new dog tags bearing the name “Wolverine,” inspired by a story Kayla shared with him.
Following the procedure, Logan finds himself a pawn in Stryker’s twisted game, as the major seeks to erase Logan's memories and utilize his DNA to create a new weapon. But Logan’s fierce desire for self-preservation ignites, driving him to escape and hunt down Stryker. In this pursuit, he encounters deadly foes, including Zero, and allies with Gambit, who assists him in locating Stryker’s lab.
As events unfold, Logan discovers shocking truths about Kayla's betrayal and Victor's ambitions. What ensues is a chaotic clash involving the activation of Weapon XI, Stryker's ultimate mutant killer, and a desperate rescue of freed mutants. In the resultant battles, Logan faces Victor again, leading to transformative moments of pain and sacrifice.
In a bittersweet conclusion, after the dust settles, Logan is left with fragmented memories, forging his path alone, while a glimpse of the consequences of Stryker's actions lingers, hinting at the continuation of chaos in the wake of his experiments. In the end, Logan's journey encapsulates the trials of love, betrayal, and an unyielding quest for identity amidst a backdrop of war and betrayal.
