Project WideAwake was a covert CIA task force President Kennedy's administration authorized following the Cuban Missile Crisis to investigate other X-Gene cases and their prevalence across the United States.
While its mission strictly revolved around identification and research of mutants, it did have the ability to exercise paramilitary autonomy from the President's mandates.
Records state that in July 1963, Azazel and Tempest were ambushed by Project: WideAwake operatives, and died in the firefight that followed.
A folder for Project WideAwake also appears on Stryker's computer in X2.