William Stryker has Victor kidnap mutant children for their abilities, including Scott Summers to the mutant prison on Three Mile Island. Stryker convinces Logan that he can help him kill Sabertooth by infusing him with adamantium. Stryker binds Logan's bones with adamantium, and he flat lines afterwards. After a few moments, though, he resuscitates and escapes the facility after overhearing Stryker order that his memories be erased for so that his DNA could be used for an upcoming project. Stryker used Wade Wilson body, who was killed by Sabretooth, and gathered and collected the DNA from mutants whose powers could be used collectively within one body without destroying it, with Wade being the host body. By then, Wade was gone, and was now known as Weapon XI, "The Mutant Killer" - Deadpool. Stryker also seals Wade's mouth and gives him an Adamantium skeleton.
Wolverine is captured by William Stryker and taken to Alkali Lake, for Weapon X.
After capturing Moira MacTaggert, Beast, Mystique and Quicksilver, William Stryker takes them to Alkali Lake. Scott Summers, Jean Grey and Kurt Wagner discover Logan (dubbed Weapon X), and Jean frees him with her powers as Logan/Weapon X attacks the guards. Meanwhile, Stryker escapes via helicopter while Logan tries to attack Scott and Kurt, although Jean calms him down and restores a part of his memory, just enough to give him sanity and allows him to escape into the wilderness.
The Weapon X Program is reopened by a secret government agency, it begin creating mutants through brutal and sadistic methods, to sell off to the highest bidder. Angel Dust and Ajax are among the first created, with the later becoming a doctor for the company.