GUATEMALA CITY — When the audience filed into the courtroom, they found 38 boxes in three rows, sealed with masking tape and marked “Finca Tinajas.” It was Feb. 9, the seventh day of the Sepur Zarco trial in Guatemala City’s Palace of Justice. Amid murmurs from onlookers, forensic archaeologists cut open the boxes one by one and laid out their contents as Judge Yazmin Barrios listed the new evidence for the court reporter.

“Light red underwear,” Barrios said. “Pieces of a white shirt. Pieces of fabric, coffee colored. A blouse, colored blue, with flowers.” Next to each garment, archaeologists laid little paper bags. Inside the bags were human bones dug up with the clothing from the former military base at Finca Tinajas, in northeastern Guatemala.

On one side of the courtroom, behind a row of government and NGO lawyers sat 11 elderly women from the Q’eqchi Maya communities of the Polochich Valley, in the fertile lowlands near Guatemala’s Caribbean coast. Their faces were covered with colorful scarves to hide their identities, but as the archaeologists pulled out clothing and bones, several of the women shook silently, scarves slipping to reveal lined brown faces.

Though acidic soil degraded the bones beyond possibility of identification, the implication put forth was clear: The unveiling of bones was a grim reunion. According to the prosecution, in August 1982, Guatemalan soldiers responded to a Maya land-rights campaign by raiding valley communities and taking many men — including the husbands of six of the women in the courtroom — to Finca Tinajas, never to be seen again. In the hours and days that followed, prosecutors said, soldiers forced the women into sexual and domestic slavery at a military base near the village of Sepur Zarco. In 2012 evidence to support that story was found when the body of a missing man was identified among the skeletons at Tinajas.

Sitting across the courtroom, starting alternately at the ceiling and the floor, was Heriberto Valdez Asig, a military auxiliary and municipal policeman accused of leading the raids that transported the six men to Finca Tinajas. He is being charged with their forced disappearance, a crime under Guatemalan law. Next to him sat Estheelmer Reyes Giron, a former artillery lieutenant who is charged with the murder of a Q’eqchi woman and her two children, and with committing crimes of sexual violence for his role in running the base at Sepur Zarco. Because these crimes are violations of international law, the men are also being charged with crimes against humanity.

Asig and Giron, the nameless bones and the covered women — all of it marked a bold new phase in Guatemala’s efforts to hold former military officials accountable for crimes committed during the country’s brutal civil war. During that war, which lasted from 1960 to 1996, battles between the state and Marxist guerrillas often served as impetus and cover for massacres that left an estimated 200,000 people dead and another 45,000 missing — the vast majority of them civilians. Other ongoing cases involve the discovery of 500 bodies on a different military base, the 1980 burning of the Spanish Embassy with 37 activists inside, and the forced disappearance of a teenage boy from the western city of Quetzaltenango in 1981. These cases parallel ones in other Latin American countries such as Argentina and Peru, where local prosecutor’s offices are going after former military officials for massacres and disappearances committed during their own Cold War-era dirty wars.

But Sepur Zarco was a new development, a test case in which prosecutors are attempting to prove that the wartime Guatemalan military deliberately used rape and murder as tools of war to crush grass-roots activism. This is significant not only for Guatemala but for international jurisprudence: It is the first trial of soldiers in a national court rather than by an international commission for sexual violence. That is, strategic rape, as seen in cases as varied as the Korean “comfort women” of World War II and the rape campaigns in Rwanda and the former Yugoslavia. In Guatemala the trial has made international headlines. U.S. Ambassador Todd Robinson attended the first day, tweeting his congratulations to “Guatemalan society and the Guatemalan justice system for confronting these issues.”

In the courtroom, the two sides agree on very little. To the prosecution, the nameless dead and the masked women are part of a common story of government repression. To the defense, the case is a legal lynching, a politically motivated trial of the wrong men, based on nonexistent evidence. But the display of the boxes was a theatrical reminder of one thing both sides agree on: Whatever happens, the consequences of the Sepur Zarco trial go far beyond the fate of the two men in the dock.