Weapon X was a code name for a secret US government project intended to deliberately induce superpowers for military purposes. It was only one part of a larger program called Weapon Plus. In the case of Weapon X, the mechanism was genetic engineering, specifically, creating mutations in normal humans and enhancing existing mutations. The successive projects had Roman numerals, so Weapon X was the tenth such project. Some confusion has arisen because this same name has applied to several different projects as well as several of the project's "graduates."
The first Weapon X project took place in the US in the 1960s, sponsored by the CIA. They recruited skilled intelligence operatives, who became Team X, made up of Logan (Wolverine), Silver Fox, Victor Creed (Sabretooth), Christoph Nord (Maverick), John Wraith (Kestrel), and Mastodon. Although successful at first, the team was disbanded after a mission involving Omega Red. The government's hesitation in relying on mutants may also have been a factor; they had created a group of robots (code-named Shiva) to neutralize any member who caused problems. Another mutant named Psi-Borg repressed their memories of the project, and all had received a treatment derived from Wolverine's healing ability. The Weapon X project, however, became the Pest Control Section at the Department of Agriculture, where it continued its work, albeit on a smaller scale. 
In the 1970s the Weapon X project expanded into Canada, where it was run by Department K but still funded by the CIA. The goal this time was to enhance the abilities of agents already working for Department H, including Ajax, Deadpool, Garrison Kane, Sluggo, and Slayback. Their test subjects did not fare as well as Team X, however, and many of them were permanently disabled. Even worse, these "dropouts" wound up at the Hospice, where Dr. Killebrew and Ajax performed unspeakable (and unauthorized) experiments on them. After Deadpool led an escape from the Hospice and exposed Killebrew, the entire Weapon X project in Canada was dismantled. Dr. Horatio Huxley revived the project briefly.
The American project, meanwhile, was dusted off and revitalized. The staff included "Professor" Andre Thorton and John Sublime (both veterans of the Weapon Plus program), as well as Dr. Carol Hines, Dr. Abraham Cornelius, and Dr. Dale Rice. Thorton located Wolverine and, in a secret lab (near Roanoke, Alberta province, Canada), augmented his skeleton with adamantium. Temporarily insane from pain, Wolverine massacred most of the lab personnel and escaped. Thanks to this setback, Thorton's Weapon X project lost the support of the Weapon Plus program, but Thorton continued his work.
Eventually, the Team X members recovered their repressed memories. As a result, Silver Fox (then working for HYDRA) killed Thorton; Psi-Borg killed Hines; and Maverick killed Cornelius. Despite this setback (or because of it), Sublime, the new head of Weapon Plus, brought the Weapon X project under his control. He appointed Malcolm Colcord, a survivor of the Roanoke massacre, as its new director. He gave the project two additional goals: to monitor mutants in the general population and to set up concentration camps where they would be recruited, held for study, or executed. Colcord brought in Brent Jackson (former agent of SHIELD), Sabretooth, Deadpool, Copycat, and Mauvais.
The new Weapon X team's first success was to psionically gain control of Wolverine and direct him to track down the "alumni" of previous Weapon X projects. They were forced to detain him, though, when he regained his volition. The Shiver Man freed Wolverine, upon which Colcord and the others fled.
Colcord next brought in Box to build a concentration camp called Neverland. The Weapon X project had reached the height of its power. They recruited Aurora, Sauron, Mesmero, Marrow, Wildchild, Washout, Garrison Kane, and many more mutants. Some joined willingly. Most did not.
Cable organized the Underground, a mutant movement to counter the atrocities going on at Neverland. With assistance from Agent Jackson, they led an assault on Neverland, in which Kane was killed. Jackson's help, however, was a ploy to help him take over the Weapon X project. Learning of the camp, the X-Men sent Chamber there undercover. Jackson ordered him to assassinate Sublime, at which point Chamber disappeared --as did everyone else at Neverland. The Weapon X project moved to another facility they named the Program.
Jackson scored another success when he subverted Maverick, who arrived at the Program in critical condition after a battle. In exchange for his life, Maverick agreed to another treatment and became Agent Zero. Now working for Jackson, he neutralized Marrow's team. Apparently considering the debt satisfied, he teamed with Wolverine and Fantomex (a product of the Weapon XIII project) to uncover the truth about Weapon Plus. They found Neverland and the Program abandoned but managed to track down Sublime. Only then did Wolverine learn what had happened at Roanoke.
A new Weapon X project, whose staff included Dr. Martin Sutter, Dr. Sarah Kinney, and Dr. Zander Rice (son of Dale Rice), followed. They produced Native, who was rescued by Wolverine and Sabretooth, and a female clone of Wolverine, X-23, who escaped after killing Rice and Kinney.
Currently, Colcord and Jackson appear to be running separate, competing Weapon X projects. Also, Nathaniel Essex (Mister Sinister) is still working with the project, using the name Dr. Robert Windsor. Sinister's journal, chronicling his experiments in a Nazi death camp, inspired Thorton to work on one of the original projects; the full extent of Sinister's influence on the Weapon X programs is still unknown.
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Weapons: None known.
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