Against a long history of impunity, a Guatemalan high judge last month sent to trial a lingering genocide case against a popular former dictator who presided over the most brutal phase of repression during the country’s 36-year civil war.

Until last year, Efraín Ríos Montt, now 86, has avoided indictment through government agencies still loyal to the former dictator, and by his status as a Guatemalan lawmaker and law that exempts members of Parliament from prosecution.

But when his term expired and he failed reelection in 2011, a Guatemalan judge hearing cases against former Ríos Montt operatives on genocide and crimes against humanity saw enough evidence of Ríos Montt’s own involvement to indict him in January 2012 on the same charges. Under Ríos Montt, Guatemala’s Army in 1982-83 carried out a series of “scorched earth” massacres against Ixil Maya in the El Quiché region of Guatemala as part of its campaign against insurgents, where civilians were rounded up, tortured, raped, dismembered, and then killed or disappeared. “We can establish these are acts so degrading, so humiliating that there is no justification,” Judge Patricia Flores said to Ríos Montt in her ruling. “You were the general commander of the military and had knowledge of the execution of these plans.”

Four months later, in May 2012, Ríos Montt was indicted on a second and separate charge of genocide and crimes against humanity when Judge Flores found sufficient evidence that Ríos Montt “knew of, controlled, coordinated and supervised the Army’s plans” during the 1982 3-day massacre of Dos Erres Mayans.

After a year of delays brought by defense motions and appeals, Judge Miguel Ángel Gálvez reactivated the Ixil case last month, rejecting claims that Ríos Montt is amnestied through the country’s National Reconciliation Law.

“The evidence against Ríos Montt is solid and the case is very well argued,” Orlando Lopez, lead prosecutor on the State’s case against Ríos Montt, wrote by email the week of the January 28 ruling.

Ríos Montt’s defense for what he has called “excesses” committed during his reign has always been that he was an uninformed and uninvolved leader trying to bring peace to a country under siege, that soldiers had acted on their own in the atrocities. “His intention was only to restore order and cooperation among the Mayan-Ixil,” Ríos Montt’s lawyer has said of his client. “He did not determine the level of force that the Army used.”

But a packet of documents that surfaced in 2009, entitled “Operacion Sofia,” that details the Army’s 1982 Ixil operations, says otherwise, according to experts. The packet consists of 359 pages of plans, orders, maps, telegrams and hand-written reports. “These records show chain of command communications up and down the line, and coincide with witness testimony,” said Kate Doyle, the forensic archivist who was given the documents by Guatemalan sources. “They provide firsthand evidence of Ríos Montt’s deliberate policy of repression and terror against the Ixil Mayans. But it should be emphasized that they became available to prosecutors not from the Guatemalan government but through leaks and accidental discoveries.”

More than a decade of efforts to prosecute Ríos Montt for human rights violations produced during his fourteen month reign have been hindered by State prosecutors conditioned by impunity and inefficiency, and by a legacy legal process that makes it easy for defendants to delay cases indefinitely.

A 2010 Human Rights Watch report found that Guatemala’s courts “routinely fail to resolve judicial appeals and motions in a timely manner, and allow defense attorneys to engage in dilatory legal maneuvering.” “The army and other state institutions resist cooperating fully with investigations … and the police regularly fail to provide adequate protection to judges, prosecutors, and witnesses involved in [atrocity] cases.”

But recent changes in the country’s judicial system, which separate out high risk cases and assigns them to the most competent judges least prone to outside influence, and a new Prosecutor General more focused on resolving Guatemala’s most serious human rights cases, have produced results. Claudia Paz y Paz Bailey, who took control of the Public Prosecutor’s office in 2010, has received international recognition for her work toward judicial independence. “She is not afraid of these cases, and she knows how to move them,” said Naomi Roht-Arriaza, law professor at the University of California, Hastings, and an expert on Latin American genocide cases. “She’s gotten rid of nonperformers [in the Public Prosecutor’s office] and those influenced by the Army, or who have political ties. She is committed to changing the impunity culture in Guatemala’s legal system, and has been absolutely instrumental in these cases.”

Pressure also from the UN and from the Inter-American Court of Human Rights, and the persistence of victims groups has factored in Guatemala’s prosecution of crimes produced by its civil war. “The fact that this case is moving forward is a testament to the endurance and bravery of the witnesses, the prosecutors, the judges, and grassroots movements that are determined to see justice done,” according to Kelsey Alford-Jones, Director of the Guatemalan Human Rights Commission in Washington DC.

Inevitably, the issue of what constitutes genocide will become central in the case against Ríos Montt. “During the war there were deaths, excesses and even massacres, but not genocide,” Ríos Montt’s lawyer has claimed. In defending Ríos Montt against the charge of genocide, his defense is expected to argue that other areas of Mayan concentration were left untouched by the Army, and that non-Mayans were also killed during the war.

“But this is not a case about the genocide of Mayans in general,” said Ms. Roht-Arriaza. “This is a case about the annihilation of a specific group of Mayans perceived to be particularly unruly and defiant, who could not be pacified, where entire villages were razed to the ground, where the Army viewed them as seeds of subversion and felt they had to kill them all. That’s genocide.”

Guatemala’s 1960-1996 civil war was the culmination of an anti-government solidarity that had been building among the country’s marginalized in the early 1950s. Land and labor reforms brought by a reformist president in 1953 were rolled back following a U.S.-sponsored coup d’état that removed the new president and replaced him with a U.S.-loyalist military dictator. What followed, according to a UN-sponsored Truth Commission, was a “counterinsurgency turned genocide”. The repression’s bloodiest period came in the fourteen months that Efrain Ríos Montt held power. Though he was one of twelve Guatemalan leaders who presided over the country’s “whirlwind of death,” Ríos Montt massacred in the most savage and humiliating ways, and brought a precision and discipline to group slaying. In the end, 250,000 Guatemalan citizens were slaughtered or disappeared in the conflict.

Ríos Montt began his rise to power as an army cadet in 1946. In 1950 he attended the U.S. Army’s School of the Americas, established in 1946 to train Latin American militaries in counterinsurgency techniques, commando and psychological warfare, military intelligence and interrogation tactics. In 1970 he had been made Army Chief of Staff, and in 1972 had risen to the rank of Brigadier General.

In 1974 he ran for President, representing the rightist National Opposition Front, and lost despite winning a majority vote. He claimed electoral fraud and the influence of Catholic priests on the electoral board, who had made an issue of his Army’s treatment of Catholic Mayans. As consolation, Ríos Montt was paid a sum of money and exiled to Spain as a military attaché. In 1977 he returned, retired from active military service, and began preaching under a rightist U.S.-based Fundamentalist church he had joined.

But the want for power remerged, and in 1982 Ríos Montt and disgruntled Army officers seized control of Guatemala by coup, whereupon he turned his attention to eradicating once-and-for-all the pestering reform movement dividing the country. He declared a one month amnesty period during which revolutionaries could surrender themselves. But when his amnesty was rejected, Ríos Montt was ready to act swiftly and harshly, as if he’d been waiting for justification for what was to follow. “Listen well, Guatemalans,” he warned the country on June 30, 1982. “We are going to combat the subversives by whatever means we want … totally just, but at the same time with energy and vigor … We are prepared to change Guatemala, we are prepared to do so with honesty and justice … peace and respect for those who are peaceful and respect the law, prison and death to those who plant criminality, violence and treachery.” Thus began what came to be known as the scorched-earth campaign, where rural Mayans were brutalized and killed, and their villages burnt to the ground and depleted of all life including crops and livestock to eliminate any possibility of recovery.

In August 1983, after 14 months in power, Ríos Montt was overtaken in a coup led by his own minister of defense.