Operation Condor
Some people know of Augusto Pincochet, and his military dictatorship that killed and tortured thousands in Chile, but many do not know that he was only a small part in right-wing dictatorships in South America propped up by the U.S. government and the CIA. Operation Condor was a clandestine operation that the United States was forced to declassify after Pinochet was extradited to Spain for his role in the torture and murder of Spanish citizens.
To put it simply, Operation Condor was a blank check given to South American dictatorships to silence dissent in their countries. It is estimated in the Archives of Terror that at least 50,000 were killed, mainly in Argentina under General Jorge Rafeal Videla, and over 400,000 imprisoned in total. Many of these dictatorships also several international fugitives from justice, like the military junta of Paraguay allowed Nazi war criminal Josef Mengela in the country to seek refuge.
This was one of the longest CIA operations carried out, in terms of time and countries affected. The U.S government only declassified it until it had to, and was officially halted with the fall of the Berlin wall in 1989. Who knows what other countries are affected today by other operations?