The origins of COINTELPRO were rooted in the Bureau's operations against hostile foreign intelligence services. Counterintelligence, of course, goes beyond investigation; it refers to actions taken to neutralize enemy agents. 

"Counterintelligence" was a misnomer for the FBI programs, since the targets were American political dissidents, not foreign spies.  In the atmosphere of the Cold War, the American Communist Party was viewed as a serious threat to our national security.  Over the years, anti- Communist paranoia extended to civil rights, anti-war, and many other groups.  As John Edgar Hoover, longtime Director of the FBI, put it

"The forces which are most anxious to weaken our internal security are not always easy to identify.  Communists have been trained in deceit and secretly work toward the day when they hope to replace our American way of life with a Communist dictatorship. They utilize cleverly camouflaged movements, such as peace groups and civil rights groups to achieve their sinister purposes. While they as individuals are difficult to identify, the Communist party line is clear. Its first concern is the advancement of Soviet Russia and the godless Communist cause. It is important to learn to know the enemies of the American way of life."

Although today this may sound ridiculous, the implications were deadly serious for the thousands of people who became COINTELPRO targets. After many years of investigating and disrupting these groups, the Bureau could not find evidence that any of them were foreign-controlled.