After the dissolution of Team X, only Agent Zero and Victor Creed stayed loyal to William Stryker. Wade Wilson did as well, but in secret, as he was placed in a coma. After the Wolverine became Weapon X, work on Wilson as Deadpool, aka Weapon XI began. By the time the Wolverine came to confront Stryker, Deadpool was ready for action.
Arriving on Three Mile Island, the Wolverine was attacked by Victor Creed. Defeating him, he was about to kill him until Kayla Silverfox talked him out of it. After freeing Stryker's mutant prisoners, Deadpool attacked the Wolverine. Although initially losing, the Wolverine was joined by Creed and together, the two managed to decpatiate Deadpool. Following, Stryker shot the Wolverine in the head with an Adamantium bullet, rendering him amnesic.
In the aftermath of the battle, Stryker was temporarily placed under investigation, but pardoned of all crimes. He was subsequently promoted to colonel, where he was allowed to continue his illegal activities. This led to the Battle of Alkali Lake. Several of Stryker's mutant prisoners became students at the Xavier's School for Gifted Youngsters.