Part of the broader Weapon Plus program (an initiative designed to produce Super Soldiers), Weapon X operated through Canada's Department K and was directed by Professor Thorton. At his side were Dr. Abraham Cornelius, Dr. Carol Hines and Dr. Dale Rice. John Sublime, the director of Weapon Plus, was always behind the scenes. Some of the work of Weapon X was based on the experiments detailed on the journals of Nazi scientist Nathan Essex, which were obtained by Weapon Plus after the end of World War II. The Project's original test subjects were the members of Team X, a covert ops CIA team (Wolverine/Logan, Sabretooth/Victor Creed, Maverick/Christoph Nord, Silver Fox/Kayla Silverfox, Mastodon, and Kestrel/John Wraith).
The telepath Psi-Borg (Aldo Ferro) was involved in the creation of the victims' memory implants, in exchange for being endowed with immortality. The test subjects were policed by an adaptive robot enforcer, called Shiva, should any of the agents go rogue. What the Weapon X scientists did not foresee is that the experimentation on Wolverine would cause him to go on a murderous rampage, which allowed the escape of the other test subjects, and caused the deaths of the Professor and Dale Rice, among dozens of other members of Weapon X staff, both scientists and military.
Weapon X was temporarily shut down, but eventually was reinstated. Subsequent attempts at recreating the success seen by Weapon X with Wolverine include the feral woman called the Native, Kimura and X-23, the 23rd attempt to clone Wolverine, who was designed to also hunt down rogue agents.
The Weapon X Re-Creation Project a.k.a. The Facility was headed by Director Martin Sutter, Dr. Zander Rice and Dr. Sarah Kinney. Like Weapon X once did, the Facility has also branched off from the main Weapon X Program.
Later creations of The Facility, now under the direction of Dr. Adam Harkins, include Predator X.
At some point, Weapon X branched off from Weapon Plus' control and was solely headed up by Canada's Department K. A new generation of agents were created: Deadpool, Garrison Kane (who took on the moniker "Weapon X"), Slayback, Sluggo, and Ajax, among others. Weapon X used Logan's DNA in order to endow its agents with healing powers. The batch produced many additional failures, which were sent to a facility for dissection to determine the cause of their failures.
These rejects were freed by Deadpool when he escaped from the facility. A smaller experiment was later developed by Department K with a New Zealand terrorist, who would become the third individual to be known as Weapon X, merging him with a symbiotic bacteria colony.
New Weapon X
Director Malcolm Colcord forms the third version of the Weapon X Project, designed to monitor and eliminate mutants. Colcord, once a security guard at the first Weapon X project, suffered severe facial lacerations during an escape attempt by the mutant Wolverine. Unlike the previous two installments of Weapon X, the third Project was completely U.S.-based and focused not only on the creation of living weapons, but also on the ultimate goal of Colcord, the creation of death camps. The Director initially uses Weapon X as his personal strike force to exact revenge against Wolverine. He soon begins utilizing its resources for the capturing and imprisonment of mutants in the secret government death camp called Neverland. Mutants who are not suitable to be used as military weapons would be executed, while those that are suitable are given the choice to join Weapon X or die.
A number of mutants, such as Cecilia Reyes, Maggott, Ape, Tarbaby, Leech and many others were arrested by Weapon X's agents and sent to Neverland. Those mutants deemed useless to the project were killed in gas chambers, while others were brainwashed to become Weapon X operatives. The organs of the executed prisoners were then sent to the U-Men. The agents of the third Weapon X were Agent Brent Jackson a former S.H.I.E.L.D. agent; Sabretooth, who was given new adamantium implants; the shapeshifter Copycat, Deadpool, and Mauvais.
Later on, Deadpool went rogue and new operatives were recruited into Weapon X, many of whom had their powers enhanced or were brainwashed into servitude. Maverick was saved from certain death and his powers were enhanced with the purpose of assassinating Wolverine, thus Agent Zero was created. Former member of Alpha Flight Wildchild was brainwashed and further mutated into a Nosferatu-like feral humanoid. Former mutant terrorist Marrow had her powers set to a controllable level, restoring the young woman's natural beauty. Sauron's personality was merged with that of his Karl Lykos self and his energy-draining powers enhanced so he could fire energy blasts. Garrison Kane was further transformed into a cybernetic being.
Aurora was kidnapped and brainwashed, like Madison Jeffries, who was extracted from the terrorist group known as the Zodiac and used to create hundreds of Boxbots loyal to Weapon X to serve as guards at Neverland. Washout had his powers enhanced, though at a heavy cost. Each usage of his powers endangered his life and eventually, he dies trying to kill Colcord. Mesmero joins willingly, while Reaper and Wildside, former members of the Mutant Liberation Front, became agents of the program in exchange for their lives. The psychic mutant Jack-in-the-Box joins after his legs and arms were amputated. He becomes a living polygraph.
Unbeknown to all, except Sabretooth, Mister Sinister was disguised as the head scientist at the Neverland facility, Doctor Robert Windsor. As Windsor, Sinister supposedly helped some mutants escape from Neverland, but he was only taking them to his own secret labs. After some time, Brent Jackson, the only human officially on the team, took over as Director, during a mutiny by the team in conjunction with an attack by mutants from the Underground. Cable led this group, in a mission to destroy Weapon X and expose its existence and its human rights violations. Washout and Garrison Kane died in the event, while Sabretooth was washed away into the sewers after a battle with Marrow.
Marrow used the battle to escape from Weapon X, eventually taking over the Mutant Underground, now reformed as the third incarnation of Gene Nation. Colcord fled Weapon X, with the always loyal Jeffries, and Aurora as well. Director Brent Jackson's team consisted of Wildchild, Sauron, Agent Zero, Mesmero, Jack-in-the-Box, and newly recruited Chamber, whose face was restored by the program's scientists.
Chamber was originally a double agent working for the X-Men, but was subsequently brainwashed into Jackson's service. Mister Sinister, under the alias of Dr. Windsor, remains at Weapon X. At some point, Jackson's team fought with Colcord's Boxbots. Colcord regains control of Weapon X. A person claiming to be Chamber has joined a superhero team known as Excelsior, but that person turned out to be an impostor. Following M-Day, both Chamber and Mesmero are rendered powerless.
Neverland is shut down and the prisoners, either powered or depowered, are executed by hosts of Boxbots. Records of the massive executions are discovered by Beast in the Endangered Species storyline, which also hints that some of the bodies of the prisoners executed prior to M-Day were sent to Ord and used in the research to develop the cure for mutation.
Weapons of Mutant Destruction
Under the direction of Reverend William Stryker, a new Weapon X program emerged, which focused on the creation of undetectable killer cyborgs that could eventually eradicate mutantkind. These cyborgs were created from regular humans Stryker lured into his cause. As part of the process to refine their cyborgs, Weapon X targeted several mutants with special abilities of their interest, namely Logan, Sabretooth, Warpath, Domino and Lady Deathstrike.
Age of Apocalypse
Logan uses the name Weapon X instead of Wolverine. Additionally, Deadpool didn't receive his healing factor from Weapon X, but from Apocalypse.