Logan goes through the Weapon X operation to lace his skeleton with Adamantium to make him strong enough for revenge against his half-brother Victor (for killing his girlfriend and ex-teammates). During this process he takes on the code name Wolverine because of a tale Silverfox tells him before her death. Wolverine's attack on Stryker’s facility on Three Mile Island takes place. Deadpool (Wade Wilson) undergoes Weapon XI transformation. Wolverine is rendered amnesiac. Xavier shows up at Three Mile Island to take Cyclops under his wing.
Note: The original version of the movie states that 6 years pass in between Logan leaving Team X and the timeskip to his time back in Canada. Fox's official statement is that 8 years in fact passes.