The project often captures mutants and experiments on them to enhance their superpowers and also mutates baseline humans. The successive projects had Roman numerals, so Weapon X and Weapon XI were the tenth and eleventh such projects of the Weapon X program.
Sabretooth, who is working for William Stryker, kills Wade Wilson so Stryker can use Wade Wilson's body in an experiment. Sabretooth then came for Chris Bradley and killed him, so Stryker could use Bradley's DNA for the Weapon XI program. 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 gathered and collected the DNA from mutants whose powers could be used collectively within the body of Wade Wilson. 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.
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.
Wade Wilson finds out he has terminal cancer. To save his life he agrees to an experimental procedure offered from Jared Smith. He is then taken to an Weapon X facility where he is tortured until his mutant gene emerges. After being put into a chamber that deprived him of oxygen, his mutant gene emerged and he was given enhanced abilities such as a healing factor.
- Agent Zero † - Former Second in Command
- Kayla Silverfox † - Former Subordinate
- William Stryker † - Former Leader
- Abraham Cornelius † - Scientist
- Carol Frost - Scientist
- General Munson † - Former Sponsor
- Deadpool † - Former Subordinate and Experiment
- Sabretooth - Former Subordinate and Experiment
- Wolverine - Former Subordinate and Experiment
- Lady Deathstrike † - Former Subordinate and Experiment
- Alkali Lake
- Three Mile Island (original timeline)
- Mutant Workshop (revised timeline)
To be added