In the stonewashed villages dotting the banks of the Araguaia River, which skirts the eastern edge of the Amazon rain forest, outsiders are treated with caution. Wary glances and guarded tones convey that trust is hard won.

The peasants have reason to be circumspect. They have long memories.

In this remote corner of Brazil, a ferocious civil war raged more than 40 years ago between a small band of idealistic young guerrillas and a belligerent military dictatorship set on annihilating them.

Locals recall thousands of soldiers, undercover spies and summary executions. They remember being interrogated, tortured and having their homes burned down.

For many, the war has not faded, as justice was not done. Not for the military officers accused of ordering the execution of dozens of captured guerrillas; not for the peasants, many of whom remain uncompensated for their hardship; and not for the families of the rebels, most of whose bodies were hidden and never found.

Now, four decades later, as Brazil comes to terms with the legacy of its 21-year dictatorship, which ended in 1985, old scores may finally be settled. In January, federal charges were filed against two former army officers, Lício Maciel and Sebastião Curió Rodrigues de Moura, who are accused of leading the merciless assault against the rebels in the dense rain forest of Araguaia.

It was a triumph for the families who have battled for 35 years to force Brazil to investigate the disappearances of their relatives during the 1972-1974 war. Following a series of legal victories, the intervention of an international human rights court and the election as president of Dilma Rousseff, a former guerrilla who was also tortured by the dictatorship, the government finally began to cooperate.

In 2011, a federal task force took over work started by the families to locate the bodies of the missing rebels. The National Truth Commission convened by Rousseff condemned the abuses of the military. And a federal amnesty commission has begun to provide recompense to some of the peasants victimized by the violence.

But despite that progress, accounting for the sins of the army remains agonizing. An amnesty law enacted by the dictatorship in 1979 exempts political crimes committed during that period from prosecution and continues to impede federal prosecutors. And because of the passage of time and attempts by the army to conceal evidence of the deaths in Araguaia, evidence and witnesses are scarce.

Like Chairman Mao, the young, educated leftists rebels of Araguaia who opposed the military takeover of Brazil in 1964 believed the road to revolution ran through the countryside. Following the model of Chinese Communists, they settled in the jungle in 1967, intending to foment an insurrection among the peasants.

The rebels lived undercover for years, in villages nestled between the rocky summits and babassu palm trees of the forest. They became locals — hunting, fishing, opening shops and bars, offering medical services and tutoring the villagers, who were among the poorest in Brazil. Using aliases, they stockpiled food, weapons and drugs.

“They never spoke about their past or why they came here,” said João de Deus Nazário de Abreu, 66. On an afternoon earlier this year, he sat in his simple home in the village of São Geraldo do Araguaia, under a poster of missing guerrillas, now all presumed dead, and alongside paraphernalia for the Brazilian Communist Party, of which most of the young rebels were members. “My ex-wife was seriously ill and they rushed to help her,” he said. “There were no medicines available, so many sick peasants ran to them.”

Abreu would later be arrested for helping the rebels and sent to a prison in the state capital, Belém, along with his wife, sister and other family members, he said. In August, he was awarded 72,000 reals ($18,000) in compensation.

“They were our friends,” he added. “They gave their blood for us and for the story of Brazil. Their story is of how they tried to liberate Brazil.”

The threat posed by the rebels to national security was minimal, but when the military learned of the plot in Araguaia by interrogating left wing activists elsewhere in Brazil, it reacted decisively. In 1972 it sent in 3,000 soldiers, the largest deployment of Brazilian troops since the Second World War, to find and subdue the roughly 80 rebels in a series of battles that became known as the Guerrilha do Araguaia. The first attempt to vanquish the uprising failed as, embarrassingly for the government, most of the rebels had disappeared into the forest and could not be identified.

A second wave saw soldiers sent in disguised as civilians, with forged identity documents. In the riverside village of Xambioá, the leader of the troops, Curió, whose viciousness in putting down the rebellion is infamous in Brazil, settled on the pseudonym Dr. Luchinni. (The moniker Curió is the name of an Amazon songbird native to this corner of the country.) His colleague Maciel went by the name Major Asdrúbal. The officers lived undercover and tried to identify the guerrillas.

By the conclusion of a blistering third military campaign in October 1974, nearly all the guerrillas had been systematically exterminated after army officers were ordered by their superiors to “eliminate” the rebels. Forty-one of the 67 rebels listed as killed by the army were executed even though the guerrillas posed no risk to troops, Curió admitted to the O Estado de S. Paulo newspaper in 2009.

The army used firebombs and napalm in an attempt to flush out the rebels, according to a military report from 1972 uncovered by Brazil’s National Truth Commission.

“This third and final campaign was characterized by intense levels of violence, especially in two respects: a definitive elimination of the guerrillas, even when rendered or captured alive, and a strong crackdown on locals in order to get information,” federal prosecutors noted in a court filing in January.

At least 12 peasants and an unknown number of soldiers also died.

Given state censorship of the media, the war was unknown to Brazil’s population at the time, with many families unaware of the fate of their loved ones.

Peasants suspected of cooperating with the rebels say they were arrested, beaten and tortured for information. The worst of the interrogations are said to have taken place at the Casa Azul — the Blue House — a primly painted blue-and-white outbuilding shaded by a garden of orange and mango trees on the grounds of a state outpost on the outskirts of Marabá, the nearest major city.

Antônio Alves de Souza, 76, said he fled his home to avoid a bombing raid intended to expel rebels from the forest. He was caught by troops who took him on a helicopter and ordered him to help locate the guerrillas. When he refused, he said, he was attacked with a machete, tied up, smeared with sugar and covered with ants.

Then he was tortured with electric shocks. An electrode was placed on his lip and another progressively on his ear, nipple and testicles, he said. Despite the pain, he said, he refused to divulge information.

Sitting in a wicker chair outside his home in Xambioá, he sighed. “It is torture to tell this story,” he said. “Every time it is a torture. We were tortured and now we are tortured again, as we have no justice.”

One of the few guerrillas to survive the final military operation was 77-year-old Micheas Gomes de Almeida, known as Zézinho do Araguaia, who escaped and lived under a false identity for the next 20 years. He lost all memory of the war and came to believe in his new identity as Antonio Pereira Oliveira, a bricklayer. It was only in 1996, when he saw a television report on the Guerrilha, that he began to remember. It took many visits to the region for him to piece together his memories.

“It was a fight for democracy,” he said. “A fight for liberty. The forces for good eventually won that fight, but even now [that] Brazil is a democracy, justice is not easy.”

The junta was responsible for the killing of at least 434 opponents across Brazil, according to the National Truth Commission, which delivered its final report in December. However, because of the 1979 amnesty law, few of the 100 living perpetrators of the abuses identified in the report have faced prosecution. The Supreme Court in 2010 rejected a petition seeking a review of the law.

Also in 1979, Diva Santana, 71, first learned that her sister Dinaelza Santana Coqueiro may have died in Araguaia. Diva, her brother and three other sisters had not heard from Dinaelza and her husband, Vandick Reidner Pereira Coqueiro, for nearly a decade. She first heard whispers about a war in the jungle from which there were no survivors from political prisoners then being released from jail.

In 1980, Santana organized a fact-finding trip to the region for the families of the 61 disappeared rebels. She has been campaigning for justice ever since. Her reward, she said, was to face a series of death threats by phone. Other activists have also faced intimidation, she said, which continued until Rousseff’s election as president.

In 1996, 69 families began legal action to force the government to investigate the whereabouts of their missing relatives. That same year, the families, working with experts from the University of Campinas in São Paulo, exhumed two bodies from within the whitewashed walls of the São João Paulo II cemetery in Xambioá. The bodies were positively identified as rebels killed in the war.

After 20 motions of objection were filed by the military and others, Brazil’s First Federal Court found in favor of the families in 2003, ordering the government to open the archives of the armed forces, investigate the circumstances of the deaths and search for the bodies. The government launched a series of appeals, which were ultimately rejected by 2009.

In response, the government began an investigation. But it featured military personnel, which made the peasants suspicious, and was criticized by the families as being biased.

A year later, in 2010, the Inter-American Court of Human Rights, an autonomous body that enforces the 1969 American Convention on Human Rights, ordered the Brazilian government to investigate and prosecute those responsible for the disappearances of 62 people in Araguaia. The court condemned Brazil for using the amnesty law to shield military officers accused of serious crimes.

This ruling, along with the election of Rousseff, led to a more serious push for justice. The federal ministries of human rights, justice and defense formed a new investigative team to locate the bodies of those killed.

Excavations by forensic pathologists, geologists and archeologists focused on the cemeteries in Xambioá and São Geraldo do Araguaia on the adjacent riverbank, where it was believed many of the victims were buried. Although 27 skeletons were exhumed, no new victims could be identified, only the two found in 1996.

“Ours is a fight without truce,” Santana said. “The laws in Brazil always favor those who hold economic power and, according to some experts, the amnesty law forgave these crimes. But torture is a heinous crime against humanity, as is concealment of corpses and kidnappings. These crimes should not be pardonable.”

The investigation was concurrent with, but independent from, the work of the National Truth Commission, which in its report argued that the amnesty law should not apply because of the grave nature of the crimes.

In January, federal prosecutors charged Maciel with the murder of three rebels and Curió with helping to conceal the bodies. The charges were rejected by a federal court because of the amnesty law but are pending on appeal. In 2012, Curió had been charged with kidnapping five rebels and Maciel with one. Those charges were likewise rejected and are also pending on appeal. The two deny wrongdoing.

The latest charges relate to alleged murders on Oct. 13, 1973, in the village of São Domingos do Araguaia. The military ambushed three rebels while they were breaking camp, the court filing said. Witnesses cited in legal documents talk of how the “army arrived firing machine guns.” Prosecutors also cite a passage in a book written by Maciel about the Guerrilha do Araguaia in which he admits being less than two meters away when one of the rebels was killed.

A key witness in the case is Manoel Leal Lima, a peasant who served as a guide for the army. But, so many years later, prosecutors face a struggle to prove the charges, with few witnesses and the government still unwilling to release many documents.

Last year, former Col. Malhães Paulo told the Truth Commission he had overseen an operation to “cleanse” the bodies of the guerrillas that were dug up by damaging their fingertips and dental arches to prevent identification. The bodies were then placed in plastic bags full of stones and thrown in a nearby river, he said. The families believe this is the reason most of the rebels are still missing.

If convicted, Maciel could face 12 to 30 years prison for the murder charges and — along with Curió, who prosecutors say was “responsible for coordinating the removal of bodies from graves and burying them elsewhere” — one to three years for concealing the bodies.

Prosecutors have requested that the accused pay compensation to the victims’ families and be stripped of their army pensions and medals.

At his neatly decorated apartment in Leblon, a beach district in Rio de Janeiro, Maciel was unrepentant about his role in the Guerrilha. At 85, he bears the physical scars of his battles: a nose broken in several places.

“I am not proud,” he said, holding up a compass he said belonged to a defeated guerrilla. “But we did not lose anything when these people died. They did not want democracy. They wanted communism. They were criminals.”

When asked about Curió, he laughed. “He was on a different squad. I used to joke with him. ‘Have you not found any of them yet? Come with me and you’ll have more luck!’ ”

Maciel said he believes the prosecutors will have a difficult time winning a conviction. “The Brazilian people still support the army. I am not scared. The amnesty law is a line that cannot be crossed.”

Curió could not be reached for comment.

With hammocks swaying gently in the morning breeze, four peasants who lived through the Guerrilha gathered in a cottage in the village of São Domingos do Araguaia. Once a forest outpost, it is now a truck stop town amid deforested fields. But it retains echoes of the past. In elections for state deputies in 2014, the Brazilian Communist Party polled 11.93 percent here, compared with 2.3 percent statewide.

All four were among the 700 peasants who for the past 12 years have sought compensation from the government for being arrested, tortured or run from their homes.

In August, a federal amnesty commission granted compensation to 31 of the villagers, bringing the total number to 97. But another 156 cases were rejected. And, 41 years on, more than 450 such cases are outstanding.

For the peasants, memories are still raw. Agenor Moraes da Silva, 74, said he witnessed the killing of rebels and still remembers the day Curió and other soldiers invaded his house and threatened him. Now, he needs treatment for prostate cancer but, without compensation, is struggling to pay for it.

“I was 27 then. I was young, I had talent, I had force,” he said. “And now I am 74 and I have yet to receive any compensation. Is that fair?”

Many of the other peasants face severe hardship in the absence of recompense. “We are dying, but the hope dies last,” said Maria Socorro Moraes, 63, whose family lost their farmland in the war. In August, she was finally awarded compensation.

“Time is our worst enemy,” said Sezostrys Alves da Costa, president of the Association of the Tortured in the Guerrilha do Araguaia, which has led the legal fight to compensate peasants. “Most are already elderly and debilitated. But we believe in the political will and wisdom of this government to recognize their persecution and the need to restore their dignity.”

(Photography by Mauricio Lima)