The long-expected military coup finally came in March of 1976, and so twentieth-century Argentine history entered its darkest phase. Under General Jorge Videla , a military junta initiated what it termed the Process of National Reorganization (usually known as the Proceso ), which is more often referred to as the Guerra Sucia, or Dirty War.

In the minds of the military, there was only one response to guerrilla opposition: an iron fist. Any attempt to combat it through the normal judicial process was seen as superfluous and sure to result in failure. They therefore bypassed this and suspended the Constitution, unleashing a campaign of systematic violence with the full apparatus of the state at their disposal. In the language of chauvinistic patriotism, they invoked the Doctrine of National Security to justify what they saw as part of the war against international Communism. These events were set against the background of Cold War politics, and the generals received covert CIA support. Apart from guerrillas and anyone suspected of harbouring guerrilla sympathies, those who were targeted included liberal intellectuals, journalists, psychologists, Jews, Marxists, trade unionists, atheists and anyone who, in the words of Videla, "spreads ideas that are contrary to Western and Christian civilization".

The most notorious tactic was to send hit squads to make people "disappear". Once seized, these desaparecidos simply ceased to exist - no one knew who abducted them or where they were, and all writs of habeas corpus were ignored. In fact, the desaparecidos were taken to secret detention camps - places like the infamous Navy Mechanics School (ESMA) - where they were subjected to torture, rape and, usually, execution. Many victims were taken up in planes and thrown, drugged and weighted with concrete, into the River Plate. Most victims were aged between their late teens and thirties, but no one was exempt, including pregnant women and the handicapped. Jacobo Timerman, in Prisoner Without a Name, Cell Without a Number (1981), an account of his experiences in a torture centre, gives an insight into the mind of one of his interrogators, who told him: "Only God gives and takes life. But God is busy elsewhere, and we're the ones who must undertake this task in Argentina." Adolfo Pérez Esquivel, a practitioner of non-violence, was detained and tortured - which didn't do much for the military junta's PR, since he was awarded the Nobel Peace Prize in 1980 on issues unrelated to Argentina, and had already been a nominee when he was taken in.

In the midst of this, the armed forces had the opportunity to demonstrate the "success" of their regime to the world, by hosting the 1978 World Cup . Though victory of the Argentine team in the final stoked nationalist pride, few observers were fooled into seeing this as a reflection of the achievements of the military. Indeed, the event backfired on the military in other ways. The vast expense of hosting the project (some $700 million - money sorely needed for other social development projects) exacerbated the national debt and compounded the regime's economic problems. In addition, it provided a forum for human-rights advocates, including a courageous new group called the Madres de Plaza de Mayo , to bring the issue of the desaparecidos to the attention of the international media. The Mothers of the Plaza de Mayo were one of the few groups to challenge the regime directly, organizing silent weekly demonstrations in Buenos Aires' historic central square demanding to know the whereabouts of their missing family members. Their protests have continued to the present day.

By the end of 1978, the most brutal phase of the violence had finished and the guerrilla movements had been effectively smashed, though the disappearances continued, and Argentina remained gripped by a climate of suspicion and fear. A slight softening of Videla's extremist stance came when General Roberto Viola took control of the army in 1978 and then the presidency of the junta in 1981. That same year, hardliners under General Leopoldo Galtieri forced him out. The military's grip on the country, by this time, was beginning to look increasingly shaky, with the economy in severe recession, skyrocketing interest rates, and the first mass demonstrations against the regime since its imposition in 1976. Galtieri, with no other cards left to play, chose this moment, April 2, 1982, to play his trump: an invasion of the Falkland Islands , or Islas Malvinas as they are known to the Argentines. Nothing could have been more certain to bring a unified sense of purpose to the nation, and the population reacted with ecstatic delight. This, however, soon turned to dismay when people realized that the British government was prepared to go to war to reconquer the islands, and Argentine forces had been defeated by mid-June. The military had proved incapable of mastering politics, they had proved disastrous stewards of the economy, and now they had suffered ignominious failure doing what they were supposed to be specialists at: fighting a foreign enemy. Perhaps the only positive thing to come out of this futile war was that it was the final spur for Argentines to throw off the shackles of their unwanted military regime.

While the junta prepared to hand over to civilian control, General Reynaldo Bignone , successor to Galtieri, issued a decree that pronounced an amnesty for all members of the armed forces for any alleged human-rights atrocity.