Doctor Valerie Cooper was employed out of school by an organization she believed to be a government agency, actually the subversive Secret Empire. Later, Cooper became Special Assistant to the National Security Advisor of the U.S. President, Judge Richard Petrie, due to her driving concern about dangerous superhuman activity in the United States. Cooper believed that superhuman mutants were emerging throughout the world and that both governments and private interests had begun to exploit their abilities. Furthermore, Cooper disapproved of superhuman crime fighters operating without United States government approval. Hence, she was a prime supporter of the Mutant Powers Registration Act, though it was later repealed by the government after public outcry against it.
Cooper also wanted the United States government to be able to protect itself from superhuman mutants, and to fight back if necessary. She saw the United States as being in a mutant “arms race” with other nations to develop an effective superhuman mutant corps of its own before they do. Selected to serve with the Presidential Commission on Superhuman Activities, Cooper recruited her old college friend Julia Carpenter for an experimental procedure to create superhuman powers, resulting in Carpenter becoming Spider-Woman, and employed the Brotherhood of Evil Mutants as the government-sanctioned Freedom Force. Cooper was also involved in the Commission’s assertion of U.S. government control over the identity and property of “Captain America,” supervising the recruitment and training of a new Captain America, John Walker, and his then-partner Battlestar, as well as employing the mutant technosmith Forge to devise means for the government to detect superhumanly-powered individuals. Following the death of Commission chairperson Douglas Rockwell, Cooper replaced him and, as her first act, reinstated Steve Rogers as Captain America.
Freedom Force was abandoned by the government after being compromised during a mission in Kuwait; however, Cooper still believed that the concept of such a team was still viable, and soon after made a second attempt with X-Factor, recruiting mutant veterans of the X-Men and related teams. Cooper acted as government liaison to the team, but eventually she was forced to implement policy that she disagreed with, such as allowing the mutant terrorists Mystique and Sabretooth to join. During X-Factor’s clash with the Acolytes of Magneto, Cooper became an unwilling servant of the Acolytes. Aware of her actions but unable to control them, Cooper kept from X-Factor the fact that the government was stockpiling mutant-hunting Sentinel robots. When X-Factor learned this, they left government service. Still, Cooper kept close ties with the team and often cooperated with them on their missions. However, as government-mutant relations deteriorated, Cooper ultimately sided with the government against her former allies. This was later evidenced by her taking X-Men founder Professor Xavier into protective custody after he unwittingly created the psionic creature Onslaught. Cooper later aided the X-Men after they broke into the Pentagon searching for scientist Doctor Peter Corbeau.
When Baron Wolfgang von Strucker mind-controlled N.S.A. agent Henry Gyrich into conspiring to kill the world’s superhumans, Cooper had the Commission join forces with the V-Battalion to create the Redeemers, a team composed primarily of ex-criminals, who were promised pardons in exchange for foiling Gyrich’s plan. They succeeded with the aid of the Thunderbolts, another team of ex-criminals. Cooper granted the Thunderbolts Presidential pardons in exchange for their leader Hawkeye serving jail time.
Cooper later addressed a summit of world leaders on the growing mutant population and the Commission’s proposal that mutants be classified as weapons of mass destruction and dealt with accordingly. After meeting with the X-Man Storm, Cooper and her global counterparts gave Storm official sanction to establish the X-Treme Sanctions Executive global mutant police force. Cooper then established the Office of National Emergency; however, in the wake of "M-Day", command was given to General Demetrius Lazer. Currently, Cooper is trying to recruit the current X-Factor team, but the team does not agree.