In 1845 James Howlett sees his father (Peter O'Brien) killed by Victor Creed's father (Aaron Jeffery). In an act of vengeance, James kills the elder Creed using bone claws which protrude from his hands. With his dying breath, Creed tells James that he is also his son. James and Victor then run away. In the following years, adult brothers James (Hugh Jackman) and Victor (Liev Schreiber) are seen fighting together throughout the American Civil War, World War I, World War II, and eventually the Vietnam War. In Vietnam, Victor attacks a superior officer and is sentenced to death, along with his brother, although they survive the firing squad due to their regenerative abilities and are imprisoned.
William Stryker (Danny Huston) then approaches the two mutants and offers them membership in his Team X. The team consists of mutantsFred Dukes (Kevin Durand), John Wraith (will.i.am), Chris Bradley (Dominic Monaghan), as well as expert marksman David "Agent Zero" North(Daniel Henney) and martial artist Wade Wilson (Ryan Reynolds). The brothers join the group, and Stryker sends it to search for the source ofadamantium. After an incident in Nigeria where Stryker orders the team to kill innocent civilians, however, Logan refuses and abandons the team.
Years later, Logan is working as a logger in Canada. He lives with love interest Kayla Silverfox (Lynn Collins). Meanwhile, Victor hunts down and murders Bradley. Stryker locates Logan, and claims that someone is out to kill members of the now-disbanded Team X. Stryker asks Logan for help, but he refuses. Shortly thereafter, Silverfox is murdered by Victor. Logan, seeking revenge, hunts down his half-brother and challenges him, but is easily defeated and left for dead. Stryker again locates Logan, and this time the mutant accepts Stryker's offer.
Revealing that he has found the adamantium source, Stryker has Logan's skeletal system reinforced with the metal. After the procedure, Stryker orders his mind to be erased. Wolverine hears this and flees. Stryker orders Agent Zero to capture him.
A couple find Wolverine taking shelter in their barn. The couple give Wolverine hospitality until the next morning, only to be shot by Agent Zero. Wolverine flees, and eventually destroys the helicopter pursuing him, along with Agent Zero, before heading to Las Vegas. Wolverine locates two former associates, John Wraith and Fred Dukes, seeking to learn the location of Creed and Stryker's new laboratory.
Dukes reveals that a mutant, Remy "Gambit" LeBeau (Taylor Kitsch), had who escaped from the island and would know the location. Wolverine learns that the old team had been tasked with capturing numerous mutants, which was the reason why Wraith had left the group.
Wolverine finds Gambit in a New Orleans bar, but is blown out of the bar after confronting him. He reencounters Victor, who had just killed Wraith. Superior to his brother now, James outmatches him, but before he can kill him, he is attacked again by Gambit. Victor flees in the distraction, and Wolverine is eventually able to convince Gambit to take him to Stryker's island.
Gambit flies and drops off Wolverine at the location, Three Mile Island. There, Wolverine confronts Stryker, where he learns Silverfox is still alive; she had faked her death to lure Wolverine into becoming Weapon X, only because her deal with Stryker was that he would release her captive mutant sister, Emma Frost (Tahyna Tozzi). Wolverine departs, and Victor emerges, and threatens to kill Silverfox. Upon hearing her scream, Wolverine returns and attacks his brother.
Easily defeating Victor, Wolverine realizes he is not like him and again departs, where Silverfox explains everything to him. Wolverine then agrees to help Silverfox find the captive mutants and free them. Angered, Stryker prematurely orders Weapon XI to be activated, to find and kill Wolverine. The weapon has become a Deadpool of mutant powers, which Stryker had gathered from his captives, including Wolverine. Wolverine orders the mutants to flee while he fights Deadpool, during which Silverfox is lethally injured. The others mutants escape in Professor Xaviers (Patrick Stewart) helicopter.
Meanwhile, Wolverine and Victor, working together, are able to defeat Weapon XI. Victor flees the island afterward, and Gambit returns. Wolverine orders Gambit to ensure the prisoners are safe, while he returns to find Silverfox, who had stayed behind. Wolverine is attacked by Stryker with a gun loaded with adamantium bullets, which knock him unconscious and cause amnesia.
Silverfox uses her powers of persuasion to have Stryker walk away, then dies from her injuries. Gambit then returns to give the news to Wolverine that the mutants are safe, but due to the amnesia does not remember anything. Wolverine flees the scene as the ambulances and police arrive.