In 1845, James Howlett, a boy living in Canada, witnesses his father being killed by groundskeeper Thomas Logan. Anxiety activates the boy's mutation: bone claws protrude from his knuckles and he impales Thomas, who reveals that he is James' birth father before dying. James flees along with Thomas' other son Victor Creed, who is James' half-brother and has a sharp claw-nails and healing factor mutation like James. They spend the next century as soldiers, fighting in the American Civil War, both World Wars and the Vietnam War in 1973. In Vietnam, the increasingly violent Victor attempts to rape a Vietnamese woman and kills a senior officer who tries to stop him. James returns to Victor upon the commotion, and ignorant of his brother's intent, he rushes to defend him. This results in the pair being sentenced to execution by firing squad, which they survive due to their mutant healing abilities. Major William Stryker approaches them in military custody and offers them membership in Team X, a group of mutants including Agent Zero, Wade Wilson, John Wraith, Fred Dukes and Chris Bradley. They join the team for a few missions, with James using the alias Logan, but Victor and the group's lack of empathy for human life causes Logan to leave.
Six years later, in 1979, Logan works as a logger in Canada, where he lives with his girlfriend Kayla Silverfox. Stryker and Zero approach Logan, reporting that Wade and Bradley have been killed; someone is targeting the team. Logan refuses to rejoin Stryker, but after finding Kayla's bloodied body in the woods, realizes that Victor is responsible. He finds Victor at a local bar, but Logan loses the subsequent fight. Afterward, Stryker explains that Victor has gone rogue and offers Logan a way to become strong enough to get his revenge. Logan undergoes a painful operation to reinforce his skeleton with adamantium, a virtually indestructible metal. Once the procedure is complete, Stryker orders that Logan's memory be erased so he can be used as Stryker's personal weapon, but Logan overhears and escapes to a nearby farm, where an elderly couple takes him in. Zero kills the couple the following morning and tries to kill Logan, but Logan takes down Zero's helicopter and swears to kill both Stryker and Victor.
Logan locates John and Fred at a boxing club. Fred explains that Victor still works for Stryker, hunting down mutants for Stryker to experiment on at his new laboratory, located at a place called "The Island". Fred mentions Remy "Gambit" LeBeau, the only one who escaped from the island and therefore knows its location. John and Logan find LeBeau in New Orleans, then both fight Victor, who kills John and extracts his DNA. Agreeing to help release mutants that Stryker has captured, Gambit takes Logan to Stryker's facility on Three Mile Island. Logan learns that Kayla is alive, having been forced by Stryker into surveilling him in exchange for her sister's safety. However, Stryker refuses to release her sister and denies Victor the adamantium bonding promised for his service, claiming that test results revealed Victor would not survive the operation. Stryker activates Wade, now known as Weapon XI, a "mutant killer" with the powers of multiple mutants.