In a future where mutants are nearly extinct, an elderly and weary Logan leads a quiet life. His healing powers are fading and he spends his days as a limo driver in a border town. But when a young mutant girl with extraordinary powers named Laura comes along, he is tasked with protecting her from dark forces who want to capture her. As they embark on a dangerous journey to reach a safe haven for mutants, Logan must confront his own demons and rediscover his purpose.

The film follows the early years of James Logan, also known as Wolverine, as he navigates his complicated relationship with his brother Victor Creed. They both serve in the American Civil War, World Wars, and the Vietnam War, thanks to their regenerative powers. Logan is recruited by Major William Stryker to join Team X, a group of mutants, but leaves after witnessing their brutality. Years later, Logan's girlfriend is murdered, leading him to seek revenge on Victor and confront his past. Along the way, he learns about Stryker's secret mutant prison and laboratory, rescues imprisoned mutants, and faces off against Weapon XI, a mutant created by Stryker. In the end, Logan chooses not to kill Victor and is ultimately saved by Gambit. He develops amnesia due to an adamantium bullet but walks away, ready to face his unknown future.

Logan is summoned to Japan by an old friend and gets embroiled in a conspiracy involving yakuza and mutants. He must protect Mariko, the granddaughter of his friend, while dealing with his own mortality.