The product of a mating between his mother and a machine, Charlie-Cluster 7 was born in the World, a secret square mile of experimental micro-reality built by the military industrial complex. In the World, artificially evolved super-soldiers destined to serve mankind during the inevitable war between humans and mutants were bred and trained by the Weapon Plus Program. The World’s scientists heated up time itself until it flowed in all directions at once. Into this pliant, fast-moving substance, they introduced human test groups, whose genetic material was crudely spliced with adaptive Nano-Sentinel technology, and ran the result through half a million years of cyborg mutation in eighteen months. Charlie’s nervous system was extracted and mutated into the autonomous entity named E.V.A. The thirteenth of the Program's living “Weapons,” which counted among their earlier numbers the star-spangled Avenger Captain America as the first and the mutant hero Wolverine as the tenth, Fantomex was to serve together with Huntsman (Weapon XII), Ultimaton (Weapon XV), and others in the Super-Sentinels, a group of highly efficient mutant-hunters posing as a group of super-heroes modeled after Saturday morning cartoons.

Fantomex, however, had other plans. When Weapon Plus simulated a train crash in the Channel Tunnel linking Great Britain and France to field their two latest super-soldiers, Huntsman and Fantomex, against a group of trained mutants, Fantomex seized the opportunity to escape. Pursued by the authorities, Fantomex fled to the Paris branch of the X-Corporation, the global mutant search and rescue organization, where he met its founder, Professor Charles Xavier, and Jean Grey-Summers, then acting headmistress of the Xavier Institute. Assuming a faux-French accent and falsely claiming to be Europe’s most notorious mutant criminal, Fantomex demanded sanctuary. Concerned for the safety of the X-Corporation squad that had gone to investigate the crash, and learning that Fantomex knew of its cargo, the trio escaped in E.V.A., who had taken on a flying saucer-like shape. Fantomex subsequently revealed the existence of Weapon Plus and offered to sell Xavier more information, but only if he agreed to help stop Huntsman. Arriving back at the Tunnel, Fantomex fought his way through the army that Huntsman had assembled. He shot many that had been possessed by Huntsman’s viral mind, including X-Corporation member Darkstar. On reaching the train, Fantomex located the pod which had housed Huntsman and activated a remote detonator, killing Huntsman instantly. Discovering a second pod, Jean realized that Fantomex was actually Weapon XIII, but still allowed him to escape.

Fantomex later encountered the feral mutant Wolverine in a mutant slave trader camp in Afghanistan. Fantomex had gone there to steal a list of the richest people in the world who were engaged in the trade, intending to use it as blackmail. He also found the young Afghani mutant Dust lying unconscious after she had unwittingly slaughtered her captors. Turning her over to Wolverine, Fantomex left him to deal with the encroaching mercenaries. A short time later, Fantomex contacted Wolverine and offered him information about his past in return for aid in stopping Ultimaton. Along with Wolverine’s X-Men teammate Cyclops, the trio infiltrated the World to find time frozen and the facility decimated following an attack by the terrorist group A.I.M. After time began moving again, the heroes fought through the World’s defenses and confronted Ultimaton. They failed to defeat him, and he broke out of the World, escaping to Weapon Plus’ orbital station. Following in E.V.A., Fantomex intended to destroy the station, but before doing so he kept his promise to Wolverine by opening the complete Weapon Plus database, giving him access to the secrets of his past that had been long withheld from him by Weapon X. Sickened by what he learned, Wolverine triggered the detonation sequence and blew up the station. Fantomex and Cyclops barely managed to escape in a shuttle, and after killing Ultimaton, Wolverine was rescued by Jean. Returning to Earth to find the X-Men scattered and Manhattan under siege by a mutant impersonating their arch-foe Magneto, Cyclops recruited Fantomex, E.V.A., and a group of Xavier Institute students into an ad-hoc X-Men team to oppose the villain. Fantomex led the assault, cutting a path through the faux-Magneto’s Brotherhood and liberating Xavier, precipitating the villain’s downfall.

Resuming his crusade against Weapon Plus, Fantomex found the grave of the Program’s director, John Sublime, but found it empty, except for a slip of paper bearing the word “Roanoke.” He located the secret facility of the splinter program Weapon X and found it abandoned except for Weapon X’s Agent Zero. After a brief scuffle with no clear victor, the pair reluctantly joined forces and traveled to the site of Roanoke, a town whose inhabitants were slaughtered after Weapon X unleashed a brainwashed Wolverine on them years earlier. There, they encountered Sublime but were opposed by his U-Men and forced to flee against overwhelming odds. Believed to still be under the Program’s control, Fantomex was left for dead. Later, Fantomex was contacted by the diminutive mutant Shortpack who sought his help in assassinating mutant arms dealer Steinbeck in revenge for his killing of an agent under Shortpack’s care. Fantomex refused, not wanting to become responsible for allowing the good-natured Shortpack to become a killer. Shortpack was captured by Steinbeck soon after, and whilst investigating his disappearance the shapechanging mutant Mystique, who was working for both Xavier and Steinbeck’s ally Shepard, learned of his meeting with Fantomex. Though despising him after a past encounter in Madagascar, Mystique found Fantomex in Monte Carlo, once again operating under the pretense he was a mutant thief, and learned of Shortpack’s plan. As she left to rescue him, Fantomex followed and uncovered her intent to assassinate Xavier. In exchange for his silence, Fantomex bade Mystique perform a heist for him. After she returned with the goods, Mystique infected both Fantomex and E.V.A. with a techno-organic virus, seemingly killing them both to keep her plan secret. However, it was all a ruse as Mystique knew she was being monitored by Shepard. Fantomex later resurfaced and helped Mystique capture Shepard, giving her access to Steinbeck whom she defeated.