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Dr. Valerie Cooper was originally a special National Security Advisor on national security issues, which include metahuman affairs. Originally, Valerie Cooper took a hard-line concern on the problem of the threat that superhumans and mutants posed to the United States.
This position changed slightly when Valerie Cooper oversaw Mystique's team, the former Brotherhood of Mutants, which operated as government agents under the new name of Freedom Force. Around this time Cooper was also involved in a project to create government sponsored superheroes which resulted in the creation of the second version of Spider-Woman (Julia Carpenter) as well as three villains that would become her enemies Deathweb. Carpenter would subsequently be assigned by Cooper to join Freedom Force. Meanwhile, Valerie Cooper and the Commission were directly involved in the events of the government demanding the identity of Captain America under the argument that he was their property. With Steve Rogers giving up the identity of Captain America, Cooper supervised the recruitment of John Walker and Battlestar. The two of them became the new Captain America and the new Bucky, respectively. Valerie Cooper's next duty was to hire Forge, to create a machine to detect mutant powers. The Freedom Force project was shut down when several members were killed while others were missing after being abandoned in Kuwait. During the Muir Island Saga, Cooper's mind fell under the control of the Shadow King. Valerie was ordered by the Shadow King to shoot Mystique but fought the command and ended up turning the gun on herself. Val was critically injured, but survived. Mystique, with the aid of Nick Fury and S.H.I.E.L.D. hypnotists, went undercover as Val in an attempt to foil the Shadow King. It wasn't until the defeat of the Shadow King, by the X-Men and X-Factor, that Mystique and Cooper were able to return to their own lives.
After witnessing first-hand the deeds of mutants throughout the years, Valerie Cooper wanted to give the concept of a government sponsored team another shot. She was able to convince several members of the X-Men and their associates to form a new X-Factor team. This new team, comprised of Havok, Polaris, Wolfsbane, Multiple Man, Quicksilver, and Strong Guy replaced Freedom Force, with Val acting as government liaison to the team. Soon after Val was once again mentally controlled, this time by the Acolytes. Val was freed from the Acolytes' control, but her relationship with X-Factor was damaged when it was revealed that she knew of Project Wideawake, a new Sentinel project being developed by the U.S. Government. Cooper later decided to hand leadership of the team directly to Forge. With the world getting more dangerous around her and the departure of some of the members, Cooper was forced by the government to allow Mystique and Sabretooth to join. With Forge in command, the team went underground.
Commission on Superhuman Affairs
Cooper returned to the Commission on Superhuman Affairs. In her position, she found herself helping the X-Men out on several occasions. She was later responsible for taking Charles Xavier away to a government facility following the Onslaught incident. Valerie was instrumental in helping the old Thunderbolts defeat Henry Peter Gyrich and negotiated for the team their Presidential Pardon.
Cooper helps establish the Office of National Emergency (or O*N*E), an official government branch dedicated to preparation and defense against superhuman threats; not much later, she became its Deputy Director. The O*N*E, with its first line of defense being the Sentinel Squad O*N*E has now been called into action after the events of M-Day. Several members of the squadron regularly patrolled the grounds of the X-Mansion. O*N*E (and so Valerie) became responsible for the mutant refugee camp established at the mansion. Many mutants join the camp willingly while some are secretly coerced into it. Johnny Dee, one of the refugees, forces the mutant Leech to depower Mr. M. Dee forces Magma to kill him. This was done at the request of O*N*E commanding officer Demetrius Lazer. When Valerie Cooper questions General Lazer about this situation, she ends up with no other choice but to be brutal and break his kneecaps. O*N*E had remained at the X-Mansion even after the dissolution of the refugee camp. When the X-Men defy the Sentinels in order to rescue a weak and confused Caliban, Cooper is right there to question Xavier on exactly what went down and why. She becomes distressed at his unwillingness to tell the entire truth. With the destruction of the X-Mansion and the X-Men's subsequent move to San Francisco, O*N*E no longer watches over the X-Men's day-to-day activities nor does it guard them with Sentinels. Val also recently confronts her old friend Multiple Man when he becomes involved in the affairs of S.H.I.E.L.D. She later shows up, taking an interest in Siryn's unborn child. During a confrontation when Siryn is leaving for the hospital because her water broke, Val is accidentally shot. She is later seen recovering in hospital.