The current charges against former Chilean leader General Pinochet stem from his alleged role in the secretive plan.
Under Operation Condor, as many as six South American regimes took part in the joint campaign to hunt down and kill their left-wing opponents.
Although the conspiracy now dates back nearly 30 years, the consequences continue to cast a shadow over the present-day governments of the region.
Former Chilean President Augusto Pinochet and two other ex-leaders are still being pursued by judges on charges related to the operation, as efforts continue to find out exactly who was responsible.
Operation Condor was founded in secret and remained a mystery until after democracy had returned to South America.
It might never have come to light at all but for a chance discovery in Paraguay in December 1992.
A local judge went looking for files on a former political prisoner at a police station in the capital, Asuncion – but instead he found detailed documents that have since been dubbed the Archives of Terror.
These contained information on hundreds of Latin Americans who had been secretly kidnapped, tortured and killed by the secret services of the military regimes involved.
According to the documents Operation Condor was established at a military intelligence meeting in Chile on 25 November 1975 – Gen Pinochet’s 60th birthday.
Delegates from five other countries were there: Argentina, Brazil, Bolivia, Paraguay and Uruguay.
Following that meeting, the military governments of those nations agreed to co-operate in sending teams into other countries to track, monitor and kill their political opponents.
A joint information centre was established at the headquarters of the Chilean secret police, the Dina, in Santiago.
As a result, many left-wing opponents of military regimes in the region who had fled to neighbouring countries found themselves hunted down in exile.
But this pact apparently went far beyond Latin America, with agents of Operation Condor accused of murder plots in various other countries, including Italy and the United States.
However, Gen Pinochet denied all knowledge of Operation Condor when he was questioned by a Chilean judge.
“No, I don’t remember, because it wasn’t my problem,” he told Juan Guzman in September. “That was an issue, I imagine, for mid-level officials.”