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Sublime is a powerful villain from Marvel comics and an enemy of mutants everywhere, making it a natural enemy of Charles Xavier and the X-Men.
Sublime was the self-appointed name of a sentient bacterial lifeform that arose during the beginnings of life on Earth. With the rise of multicellular lifeforms, Sublime found endless numbers of hosts it could infect. However, mutantkind, immune to Sublime's infection, eventually arose and multiplied, becoming the first threat to Sublime's domination.
It was hinted that the very hatred and fear of mutants was caused by Sublime itself. But the bacteria took more direct actions in order to ensure that mutant population would be held in check, if not exterminated, in order to keep it from becoming the dominant species of the planet.
The first step was the Weapon Plus Project, Sublime took over a human body, dubbed Dr. John Sublime, and became the director of the Program, overseeing the creation of living weapons created by each installation of the program, from Captain America (Weapon I) to the Super-Sentinels - Fantomex, Huntsman and Ultimaton (Weapon XIII, Weapon XII and Weapon XV), passing through Nuke, Wolverine, and Deadpool, the latter two originating in the Weapon X Project, seemingly the most prolific living weapons producer.
For many years, Sublime remained behind the scenes, manipulating the Weapon Plus Project and installing Malcolm Colcord as the Director of Weapon X, which would eventually lead to the so-called War of the Programs between Colcord's replacement, Agent Brent Jackson, and Sublime, as Weapon X became an independent organization.
As millions of mutants were born worldwide, Sublime, still under the identity of John Sublime, took other steps to ensure the extermination of mutantkind. One of these steps was the creation of the TransSpecies Movement a.k.a. Homo Perfectus, outwardly a group of 'mutants born in human bodies', though actually a cult of humans that sought to empower themselves by grafting mutant body parts to their own bodies. The militant faction of this group, the U-Men, refused to have any sort of contact with the world, which they considered impure, for which they sealed themselves in containment suits.
During a trip to Hong Kong's new office of the X-Corporation, the X-Men discovered Sublime's farm of mutant prisoners, who were being harvested for mutant body parts which could give the U-Men powers. Sublime, who was in the country on a book tour, thus became aware of the X-Men's immediate threat to his plans. Sublime also planted the mutant healer Xorn in one such prison in the People's Republic of China.
Although Xorn was rescued by the X-Men, he was actually a mole. Xorn, who was revealed to apparently be Magneto, became addicted to the drug Kick (which was actually Sublime's bacterial body in concentrated doses high-enough to finally enable the infection and possession of a mutant). Xorn dealt the drug to Quentin Quire, thus placing Quire under Sublime's influence, which would cause the Open Day Riots made by the Omega Gang, and which led to the death of Sophie of the Stepford Cuckoos and Dummy, the bodiless, gaseous-form student of Xorn.
Meanwhile, Sublime and the U-Men spread their influence to New York City, where they kidnapped the telepath Martha Johansson, harvested her still-living brain, and used it as a weapon against the X-Men. Johansson resisted, and forced Sublime to fall from Emma Frost's grip to his apparent death. The Sublime organism survived, regenerated its host body, and returned to actively overseeing Weapon Plus, as always, from the shadows.
Sublime suffered a setback in its plans with the destruction of two of Weapon Plus' Super-Sentinels (Huntsman/Weapon XII and Ultimaton/Weapon XV) and the defection of Fantomex (Weapon XIII). Sublime had envisioned a team of mutant-hunters with scripted actions operating from a space station (a section of Asteroid M) in order to make the genocide of mutantkind look like a "Saturday morning cartoon come to life". Weapon XII had already been destroyed during its test-drive; Fantomex, intended to be the smart, cool member of the team refused to be anybody's weapon. Only Ultimaton remained, and even though he followed the direction of Weapon Plus operatives, he had began to question his role as a slaughter machine and was ultimately killed by Wolverine.
Under the influence of Sublime via Kick, and believing himself to be Magneto, Xorn assembled a new Brotherhood of Mutants to lay waste to the Xavier Institute and then New York City. They were defeated by the X-Men, but Xorn, under Sublime's influence, killed Jean Grey, who was manifesting the powers of the Phoenix Force. Unbeknownst to all, the Phoenix was the ultimate threat to Sublime's plan. In retaliation for Jean's murder, Xorn was beheaded by Wolverine.
Later, Chamber, an X-Man who had infiltrated Colcord's Weapon X organization, was ordered to assassinate Sublime by Brent Jackson, a S.H.I.E.L.D. agent turned Weapon X field leader. Chamber incinerated Sublime, but Sublime again regenerated. At the same time, Sublime was also responsible for sending Sabretooth against Mister Sinister in order to obtain Sinister's latest creations, the Children.
With the massive depowering of mutants following M-Day, mutantkind's threat to Sublime was greatly diminished. However, it remains to be seen if the depowered mutants lost their innate immunity to the Sublime infection.
Sublime was responsible for the birth of the Stepford Cuckoos sisters, extracting thousands of eggs from the ovaries of Emma Frost and harvesting them into humanoid/ nannite hybrids designed to kill machines. The hub of his program, the five sisters were sent to the Xavier institute to be trained in the use of their telepathic legacy.