The second hour looks at how the United States and the Soviet Union shoved international justice into the deep freeze of the Cold War, and how atrocities in conflicts with high numbers of civilian deaths—such as Vietnam, Afghanistan, and Guatemala—are covered up or ignored.
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[Indistinct voice on radio] Narrator: In fall 2014, the U.S. Immigration and Customs Enforcement Agency launched Operation No Safe Haven.
Man: His big claim to fame is that back in his country, he was in the military and apparently at one point, he killed a farmer.
Yeah, he--he did surveillance... Narrator: Its objective: the arrest of fugitive foreign nationals suspected of war crimes and human rights violations.
So, we''ll set up over there and then once this guy comes out, gets to the vehicle, we''ll go from there.
Man on radio: He is gonna be rolling out and we''re heading towards you guys, so, I''ll be behind him... Narrator: These tactics have netted a number of suspects from across the globe, including fugitive Nazis, Balkan paramilitaries, and suspected killers from the Rwandan genocide.
The target this night was suspected of crimes during conflict in Central America.
The tactics were uniquely American.
[Gavel banging] But the principle behind this operation was ratified 7 decades ago as an international obligation under the United Nations.
Man: 5 of 53, against nil, abstentions 3.
Man: What emerged from the ashes of the Holocaust was a bold attempt to bring governments together and they agreed on a new set of Geneva Conventions, they agreed on a convention to end genocide, and they agreed that any government that lent its weight to these treaties would be legally obligated to investigate war crimes.
[Man speaking indistinctly] Woman: Everyone had the idea that this was going to usher in an era of international justice.
Then the Cold War happens.
And basically, the whole project falls apart.
Narrator: The disintegration of relations between the U.S. and the Soviet Union never reached the point of direct conflict.
But over the course of 5 decades, proxy wars among nations aligned with either superpower were plagued by atrocities, which the international community had pledged to prevent.
Roht-Arriaza: There are dozens of conflicts during the Cold War era.
There are dozens of places where repressive governments shoot their own citizens, massively.
But it''s impossible for any kind of international justice to happen because one side or the other sees this as an attack on them.
Man: During our tour in the Republic of Vietnam, we have all seen what communism can do to a struggling nation and our world community.
It is therefore most important that we conduct our affairs in a manner that will show the Vietnamese citizens we are a friend, that we are here to assist them in the improvement as well as the security of this country.
Narrator: Of the numerous Cold War conflicts, the Vietnam War took an enormous toll.
In the space of 10 years, at least one million Vietnamese soldiers and civilians were killed in the north and the south.
[Gunfire] More than 58,000 American troops died in action.
At first, you''re very fearful, as you can imagine.
If you see your people killed or wounded, that''s when you become more aggressive.
And you really have to control what''s going on inside you.
That aggressiveness can turn to cruelty if you lose control of it.
Narrator: During the Vietnam War, the late Larry Colburn was a door gunner in an assault helicopter company.
On March 16, 1968, his helicopter gunship was ordered to provide air support for Charlie Company, an infantry unit that had taken casualties during recent search and destroy missions.
Colburn: The particular day of that mission, I didn''t know which village we were going into.
I didn''t know the name of it or anything else.
We were just told that it was supposed to be a VC stronghold.
Charlie Company was heavily prepped the day before, and they were seeking revenge for the people they''d lost.
Man: I volunteered to go ahead on this operation.
I heard it was supposed to be a real, you know, finally a real heavy, you know, confrontation with the VC.
Narrator: Former U.S. Army photographer Ron Haeberle was assigned to document Charlie Company''s search and destroy mission.
The target was a village known as My Lai.
I landed in My Lai about 7:50 a.m., and there were really no Viet Cong that I could spot.
The only enemy I saw that day, we had just come in from altitude to fly low-level and we caught a VC suspect in the middle of a rice paddy who was leaving the village, and he was carrying a carbine in a pack.
He made it to a tree line and got away.
That was the only Viet Cong suspect that I saw.
Narrator: On the ground, Charlie Company encountered no Viet Cong as it entered My Lai.
Nevertheless, several soldiers began shooting unarmed villagers.
As we were heading down toward Highway 521, I started to realize that something was going wrong.
Something wasn''t right.
We''re not seeing any hardcore VC, just women, old men, and children.
But yet still the GIs just kept on firing.
Anybody--they see anyone, they just fired at ''em.
It just didn''t make any sense what was going on.
As the Americans were being inserted, we saw a lot of the villagers leaving.
We left that particular part of the village, reconned around, and came back, and those same people that were leaving the village were now either dead or dying on the road.
Haeberle: As we''re entering the village, we started to see, you know, bodies laying here, laying there.
It was just unreal, because again, they''re civilians.
They weren''t, you know, combatants, [Indistinct radio transmission] Colburn: Hugh Thompson, Jr. was the pilot of the OH-23.
Mr. Thompson got on the radio and checked with other gunships that were in the area, tried to make communication with men on the ground to find out what was going on.
But we just-- we kept coming upon these piles of bodies.
Man, on radio: A lot of ... coming from that direction.
Colburn: We began marking people with smoke thinking they''d receive medical attention because they were civilians, obviously civilians.
When we''d come back to check on them, some--they''d be dead, so, we stopped marking people with smoke.
One woman, I recall, we''d marked her.
She had a chest wound. She was still very much alive.
Instead of continuing to recon, we hovered there for a few minutes because we saw a squad of Americans approaching, and Mr. Thompson wanted to see exactly what was gonna happen, so, we hovered back a little bit, and a captain approached the woman, kicked her, stepped back, and blew her away right in front of us.
That''s when we--we had to come to the terrible realization that it was our people that were killing these civilians.
I''d seen people wounded and I''d seen people killed, but I''d never seen gross numbers of civilians just murdered.
[Helicopter blades whirring] Narrator: Thompson, Colburn, and a crewmate saved 11 civilians before returning to base and reporting the massacre to their superiors.
Almost immediately, a cease-fire order was radioed to Charlie Company back in My Lai.
All remaining search and destroy missions were cancelled.
The cover-up began immediately.
A 'Stars and Stripes' headline proclaimed, 'U.S. Troops Surround Reds, Kill 128.'
Commendations were issued to dozens of troops and headquarters wired a congratulatory message, citing the company''s 'outstanding action' which 'dealt the enemy a heavy blow.'
A year after the massacre, Haeberle had returned to civilian life in Ohio and found unprocessed film that he''d taken back in My Lai.
Haeberle: I''ll never forget. I was, you know, down in the basement, you know, processing the film, hanging the rolls up to dry and that, and the My Lai roll was the last one I processed.
I remember--remember hanging that up and looking at the, you know, all the pictures on there, this--you know, I said, 'What--what should I do?'
You know, people should know what happens in Vietnam, because they read the newspaper-- 'Hey, we''re doing great. Send more troops, send more troops.'
So, I went with my photographs to the Cleveland 'Plain Dealer.'
And all havoc broke loose.
Narrator: Haeberle''s photos went from Cleveland to the world.
At the same time, independent journalists were exposing more details of the massacre.
The public outcry that followed led the Army to conduct a formal inquiry.
Jerome Walsh was a civilian lawyer assigned to the investigations.
Walsh: Every country is responsible for its own soldiers, and if these things happen, we have to--to know it and we have to bring the people to account who--who either did it or knew about it and didn''t do anything about it.
Narrator: The U.S. Army Task Force spent 4 months taking testimony from hundreds of witnesses.
Jerome Walsh went to the crime scene to interview survivors.
Walsh: I went down to My Lai for a number of days, and they would bring in these-- mostly women who had been there and could describe what had happened.
The Americans came, they shot everything that moved-- water buffaloes, chickens, babies, old men-- and then some of the women said that they weren''t from My Lai at all.
They were from another little village north of there.
So, that expanded the scope of our investigation, and then I got some people who had been over on the coast.
And these women said that they--soldiers came there and did the same thing, and they pretended they were dead, and--and they survived.
Narrator: In 1970, the officer in charge of the inquiry, General William Peers, submitted a comprehensive report on the massacre.
Peers: I have been asked about what happened in My Lai 4 on 16 March 1968, and I feel that the public is entitled to know that our inquiry clearly established that a tragedy of major proportions occurred there on that date.
Narrator: The report concluded that U.S. troops had killed over 400 unarmed civilians at their commanders'' orders.
Equally damning was the report''s conclusion of a cover-up.
Peers: Certain individuals either wittingly or unwittingly suppressed information from the incident from being passed up the chain of command.
Narrator: The report recommended courts martial for dozens of men who participated in rape, murder, and concealing truth about the event.
But by the time the Army''s criminal investigation began, most members of Charlie Company had been honorably discharged and were beyond the reach of military and civilian law.
Man: Under the law at that time, very few soldiers actually could be brought to trial because many of them were draftees serving a two-year tour, and by the time this came to light, which was more than a year after the fact, they were back in civilian life.
They couldn''t be court-martialed, and because of a gap in the law, they could not be tried by a civilian court in the United States because the crimes had taken place in--in Vietnam.
['Hail to the Chief' playing] And that was a gap that was well known to the Nixon administration and was not closed during the Nixon administration because the Nixon administration wanted the spin to be that My Lai was the work of a few bad apples, and obviously, if they had trials of 60, 70, 80 soldiers, it would expose that fallacy.
Narrator: Of the dozens of troops implicated, only two--Captain Ernest Medina and his lieutenant, William Calley, were tried.
Lieutenant Calley was the first to stand before the court martial.
Calley on recording: If I have committed a crime, the only crime that I have committed is in judgment of my values.
Apparently, I valued my troops'' lives more than I did that of the enemy.
Narrator: The crux of Calley''s defense was that he was just following his superior officer''s orders.
21 members of his unit corroborated his account.
At the second court martial, Captain Medina in turn denied that he had given those orders.
Larry Colburn testified at both trials.
I was sitting in a hallway.
I''d either just testified or I was waiting to testify.
It was Captain Medina''s trial.
They left me in a hallway by myself right next to the jury room.
The jury room door was open.
The jury was in the jury room.
A general came down the hall.
I remember looking, seeing a high-ranking officer with his entourage, and they--he walked right into the jury room.
I thought that was odd at the time.
I thought juries were supposed to be kept in private or behind a closed door.
But I heard this general walk in and say hello to some people that he knew that were on the jury, and he actually said, 'It''d be great if we could find a way to get Ernie out of this mess.'
Narrator: Captain Medina was acquitted.
Of the dozens of U.S. soldiers and officers involved in the massacre and cover-up, only Lieutenant Calley was convicted.
He was sentenced to life in prison but two days later, President Nixon ordered him placed under house arrest.
3 years later, Calley was paroled.
Larry Colburn struggled with My Lai for 4 decades.
He returned to Vietnam several times and met with survivors of the massacre.
Colburn: I think that justice will come later for the people who took part and who committed those atrocities.
If the Uniform Code of Military Justice is gonna let it go, well, then it''s--it''s up to another power.
Man: The President of the United States.
Won''t you be seated? Mr. Smith.
Woman: After the My Lai massacre, the Nixon administration set about trying to cast it as an isolated incident.
Man: In your opinion, was what happened at My Lai a massacre?
What appears was certainly a massacre, and under no circumstances was it justified.
I believe it is an isolated incident.
Certainly within this administration, we are doing everything possible to find out whether it was isolated, and so far, our investigation indicates that it was.
But behind the scenes, the administration ordered the secretaries of the Army and the other branches of the service to begin collecting all allegations of war crimes to make sure they were investigated and to report back on what they found.
Narrator: Deborah Nelson was an investigative reporter for the 'Los Angeles Times' in 2006 when independent journalist Nick Turse alerted her to documents that he''d discovered at the National Archives.
The documents, created by a secret Defense Department unit called the Vietnam War Crimes Working Group, detailed allegations of atrocities committed by American troops in southeast Asia.
Nelson: By the end of the war, the Army had compiled 9,000 pages of evidence of U.S. war crimes.
They simply took all that, locked it in a file cabinet, and walked away from it.
None of this was exposed to the public.
Narrator: Suspecting that the collection had been declassified by mistake, Nelson and her colleagues proceeded to photocopy each document.
They worked around the clock and finished the job just before the archivist reclassified and removed the documents.
But with their duplicate set safe, Nelson went on to examine each record and to enter all details into spreadsheets.
She discovered that My Lai was not an isolated event but was part of a pattern.
Nelson: Wading through 9,000 pages of gut-wrenching eyewitness testimony about the killing of civilians was one of the most difficult things I''ve ever done.
But what was the most outrageous thing to come out of those files is that nobody did anything about it.
I was a member of a 10-man ad hoc committee that monitored war crimes in Vietnam.
That was not just My Lai. That was other atrocities.
Narrator: John H. Johns is a retired Brigadier General who served on the Vietnam War Crimes Working Group.
In the early 1970s, the group assembled and assessed the records that Nelson would later uncover.
Johns: What I remember about it is that it was just cold-blooded killing, a complete breakdown of any moral code or conscience.
Narrator: Nelson and her colleagues determined that of the thousands of incidents, only 200 resulted in court martials, and only a fraction of the courts martial ended in conviction.
A few dozen American servicemen were imprisoned.
None of this was made public.
Johns: Nothing was done, and the rationale was that the Vietnam War was over and we didn''t need to rehash this with the public.
[Crowd chanting indistinctly] Man: We came here to search out and to destroy the last vestige of this barbaric war.
[Crowd cheering] Johns: You can argue that you keep people in the dark and why give critics of the United States more ammunition to hate us?
I think that was the decision that was made.
The thing that I see wrong with that is that it does not prevent it happening in the future.
[Sirens wailing] Narrator: September 11, 2001, an unprecedented attack on the U.S. homeland.
Bush: Our enemy is a radical network of terrorists, and every government that supports them.
[Applause] Narrator: Shortly after, the U.S. launched a war on terror.
Bush: In this conflict, America faces an enemy that has no regard for conventions of war or rules of morality.
Narrator: Unlike the enemy, an Islamic terrorist group called al-Qaeda, the U.S. pledged to conduct its war on terror in accordance with international law and conventions.
But personnel of the U.S. Army and the Central Intelligence Agency broke that pledge during the 2003 Iraq War... by torturing, sodomizing, and murdering Iraqi prisoners in the Abu Ghraib prison.
The abuse was documented in photographs taken by and featuring U.S. military personnel.
Like the photos of My Lai a generation earlier, these photos were distributed globally and generated global condemnation.
At the time, the Bush administration''s U.S. ambassador at large for war crimes issues was Pierre Prosper.
Prosper: I was in Iraq, I learned about it, and I remember reporting it to my boss, Secretary Powell, and--and then immediately, shortly thereafter, we had a meeting with the ICRC, the Red Cross, on--on this issue and began to, uh, think it through.
Because we''ve been out in the world pursuing accountability on various issues, so, when we are responsible, we need to get it right.
Narrator: The U.S. Congress and Defense Department both launched formal inquiries to determine the extent of prisoner abuse and command responsibility.
A few soldiers and civilians conspired to abuse and conduct egregious acts of violence against detainees and other civilians outside the bounds of international law and the Geneva Convention.
Narrator: A total of 11 soldiers were convicted in courts martial on charges ranging from dereliction of duty to aggravated assault.
The Brigadier General in charge of all detention facilities in Iraq was demoted.
An independent panel later found no evidence of a policy of abuse.
Prosper: You had the leadership commence an investigation.
You had our congressional inquiries.
You had the media that fully exposed it.
We ultimately had some--some proceedings, some court martials and so on.
So, I--so I think as a whole, when you look at accountability, the system worked.
Man: 1, 9, 1, 6.
We''re gonna have to take the detainee back... Narrator: Even as the Abu Ghraib scandal was playing out in public view, the U.S. was transporting hundreds of prisoners from Iraq, Afghanistan, and other conflict zones to U.S. military prisons at Guantanamo Bay, Cuba.
The administration of U.S. President George W. Bush called these prisoners 'detainees' and 'enemy combatants' rather than 'prisoners of war,' the legal designation.
The Bush administration had conceived these new designations to deny the prisoners the protections of international conventions and to extract intelligence from them by means of torture.
The U.S. Supreme Court rejected the administration''s practice, finding a clear violation of America''s obligations under the Geneva Convention.
Ryan: There was an attitude after 9/11 that virtually anything goes in the name of intelligence, and having lived through 9/11, I understand the--the-- the fear and the foreboding and the uncertainty and the--and the demonstrated lethal nature of al-Qaeda and its affiliates.
There''s no--there''s no minimizing that.
But we cannot have a system of justice for our enemies that is different from the system of justice that we have for ourselves, because then it''s not a system of justice at all.
Narrator: The war on terror has been marked by several efforts to exempt the U.S. and its allies from obligations under international treaties.
One of the most enduring episodes of exemption dates back to the onset of the war in Afghanistan.
It took place in November 2001, when thousands of Taliban soldiers surrendered to or were captured by the American-backed Northern Alliance.
Among the first to investigate their fate was Dr. Jennifer Leaning.
Leaning: I was concerned in January 2002 that there might be atrocities linked either to the, um, war that the Taliban had been conducting against the United States or that the United States had been conducting against the Taliban.
And we wanted to get there early to talk to people before, you know, a number of things had gotten covered up, which is always the case in the setting of active war.
Narrator: Upon arrival in northern Afghanistan, Dr. Leaning traveled to the town of Sheberghan to investigate prison conditions.
There, she began hearing rumors of a mass grave.
Leaning: We were sitting one morning with a young British aid volunteer, and he said in sort of a jolly way, 'So, you guys are here looking into prisoners of war,' and we said yes.
And he said, 'I think I passed a mass grave.'
And we said, 'Explain.'
And he said, 'Well, the Dasht-i-Leili desert.'
Narrator: The desert bordered the headquarters of an Afghan warlord named Abdul Rashid Dostum, a general of the Northern Alliance.
[Shouting in native language] Dr. Leaning and her colleagues visited the site the following morning.
Leaning: So, we drove to the Dasht-i-Leili desert.
Almost immediately, within half a mile of the outskirts of town, the driver paused and we got out.
To the right side of the vehicle as we were heading south was this vast area of turned-over sand and earth packed down with the tracks of large vehicles.
There were prayer beads scattered all over, obvious human bones, a number of prayer caps, bits of clothing.
What was surprising was how recent it was.
[Birds chirping] Narrator: The town of Fort Worth, Texas is a half a world away from Dasht-i-Leili.
But when Jennifer Leaning left Afghanistan, the investigation was continued by Dr. Nizam Peerwani while on leave from his official duties as medical examiner of Tarrant County.
Peerwani: Our objective in Dasht-i-Leili was first to identify the mass grave existed and number two was to do a test excavation to document if in fact it had human remains.
We began a shallow grave-digging until we were satisfied that we had in fact discovered a mass grave.
And the first thing that stuck us was that this was not an Islamic burial site.
It was a mass grave done by people that were trying to dispose of bodies.
Narrator: In the time allowed, Dr. Peerwani exhumed several bodies for autopsy.
It was determined that they''d suffocated.
Peerwani: We were able to say in generality that they were probably Talibans who had surrendered.
Obviously, we could not come up with any specific numbers of bodies that were buried there, but based on the-- on the test trench, we estimate there may be several hundred if not 1,000 bodies in the mass grave.
Narrator: Following Dr. Peerwani''s field exhumation, human rights investigators began amassing evidence of war crimes.
Numerous eyewitnesses claimed that mass grave victims were indeed Taliban prisoners.
They''d been suffocated or shot in steel shipping containers while being transported from one prison to another.
The alleged perpetrators were Northern Alliance fighters serving General Dostum, who collaborated closely with American troops during the war.
Man: Every one of you, from General Dostum to the soldiers that are here, you are all heroes and we were honored.
[Translator speaking] Narrator: Physicians for Human Rights presented its findings to the U.S. government and United Nations.
Leaning: We first of all debriefed with, um, high-level people in the State Department.
We spoke with the International Community of the Red Cross and U.N. authorities.
Over the years, we got very little information.
It was really hard to get anyone to listen to us.
Narrator: When the U.S. government failed to respond to Freedom of Information Act requests, Physicians for Human Rights went to court and won a wealth of diplomatic cables all indicating widespread knowledge of the massacre.
U.S. Ambassador for War Crimes Pierre Prosper advised the Bush administration on a response to the allegations.
Prosper: We did not feel that the United States government should be the one to investigate and prosecute.
We felt that the Afghans needed to play a fundamental role in the pursuit of justice because it''s part of the growth and responsibility of a democracy.
I went to Afghanistan and had conversations with various officials.
And in fact, as the conversation went on, you could hear people describing events of abuses that were 20, 25 years old.
And everyone was saying, 'Well, if you''re going to prosecute this case, you have to also prosecute events that occurred before.'
So, that began to add a complexity to the process that--that also brought this whole issue to a--a halt.
Narrator: Physicians for Human Rights and other human rights organizations have kept up the drumbeat for an investigation for the past 15 years.
Satellite imagery from 2009 indicated activity at the mass gravesite, which PHR suspects could mean the removal of evidence.
The Bush administration and the Obama administration refuse to conduct a war crime inquiry.
Rashid Dostum, now the first Vice President of the Islamic Republic of Afghanistan, has been barred from entering the United States.
Leaning: I think it''s scandalous, actually.
I am not particularly surprised by the Bush administration''s silence, because whatever occurred was under their active watch.
But the Obama administration did have the opportunity to draw a bright line and say, 'We are no longer the war government.
'We stand for human rights.
Now is the time to try to figure out what is going on.'
But when there is a failure to conduct an investigation and report out on it, that really undermines a sense that the rule of law and justice means anything.
Stover: Impunity has been the norm rather than accountability.
[Horn honking] Unless governments will face up to the crimes that they''ve committed, or willing to investigate the crimes of other countries or other governments, then we''ll never get ourselves extricated from the past.
Narrator: Increasingly, impunity is under attack, from human rights investigators determined to hold war criminals accountable for the most distant crimes.
The Guatemalan Forensic Anthropology Foundation was founded in 1991 to identify victims of a 30-year civil war... [Gunfire] [Person screaming indistinctly] Narrator: between the government and leftist guerillas, many of them from the indigenous Mayan population.
Both sides engaged in human rights violations during the war.
But the Guatemalan military and national police committed crimes on a vast scale, according to Eric Stover, who investigated human rights violations throughout Latin America.
Stover: During at least a 30-year period, there was armed insurgency, but the government used it as an excuse to repress its indigenous communities.
[Gunfire] And there was a turning of a blind eye.
There was active engagement in human rights violations, of war crimes throughout the country.
[Gunfire] Narrator: During the Cold War, countless civilians were murdered throughout Latin America by military regimes intent on destroying political opposition.
Only in Guatemala did the slaughter reach the point of genocide.
Woman: If you look at the reports that the military put out in that era about those Mayan communities, it''s very clear that they believe that the Maya across the board--men, women, and children-- were 100% supportive of the guerilla overthrow of the Guatemalan government.
And that automatically made them enemies, and therefore targets for army operations.
Narrator: Kate Doyle assesses evidence of human rights crimes at the National Security Archive in Washington, D.C.
Documents that she obtained in Guatemala have exposed the military''s campaign of violence.
These assembled units would sweep through a series of villages.
[Explosions] They would gather the population.
They would separate it by sex.
They would torture them for information.
They would typically carry out rapes and other sexual assaults.
And ultimately, they would either gun down or burn alive that village.
Man: A real homicide investigation.
You start at the crime scene, of course.
But what you have to do is take your evidence and build it into a story, the story that the evidence tells you, the story the bones tell you.
They are the witnesses.
They''re the best witnesses.
Narrator: The late Dr. Clyde Snow was a pioneer in the field of forensic anthropology.
Beginning in the mid-1980s, he and Eric Stover located mass graves in Argentina, Chile, and other countries plagued by human rights violence.
He made his first trip to Guatemala in 1991 at the request of ethnic Mayan families who had lost loved ones in the civil war.
He made his last trip there in 2013 for this film, shortly before his death.
Between those end points, he exhumed mass gravesites throughout the country.
Snow: Well, I''m asked the question pretty frequently, how long have you been a human rights advocate?
And I have to explain I''m not an advocate.
I''m an expert.
We find the evidence, then we turn it over to the advocates who fight this battle in court.
It''s hard, you know, for a revisionist to argue with a skull with a gunshot wound in the head.
Late 20s, I would.. Narrator: When established scientists in Guatemala refused to take part in exhumations, Snow enlisted students.
Fredy Peccerelli was Snow''s first assistant in Guatemala.
They began searching for massacre sites while the conflict was still going on.
I came here in January of ''95, and my first case was Cuarto Pueblo-- the massacre of 424 men, women, and children.
We found 42 100-pound sacks of bone fragments.
Narrator: Peccerelli is now director of the foundation.
He and Dr. Snow classified victims into two categories: first, the ethnic Maya; second, the urban activists, including students and labor leaders whom the military regime had designated enemies of the state.
[Gunfire] Some 45,000 of these enemies had disappeared without a trace.
By 2010, the foundation had been unable to find one.
So, Clyde and I were in his hotel room at the Holiday Inn one night, late, bottle of single malt scotch, and Clyde begins to insist, how come we haven''t found the disappeared?
How come we''re not digging? How come we''re not looking?
Where are the cemeteries they''re using to bury the unidentified?
Narrator: In search of an answer, Snow and Peccerelli came here, to La Verbena cemetery in Guatemala City.
It has served as the final resting place for generations of the urban poor.
Peccerelli: So, we came over to the cemetery, and we said, listen, we''re interested in looking at the records of all of the unidentified bodies.
They said, 'Sure, they''re right there.
Anything for you, Doctor.'
Narrator: The cemetery office only had the records from 1981 to 1986.
Peccerelli: This is January to July of ''81.
So, Clyde reached for one year, I reach for the other.
We started looking at the books.
And in a couple of minutes, you know, Clyde turns to me and says, 'I think we just solved 1,000 murders.'
See all these young 20-year-olds with gunshot wounds.
And this is their age.
Narrator: The cemetery records indicated a surge in nameless dead, arriving in the middle of the night.
Peccerelli: 24, 35, 30... You know, you could see 10 bodies found in one location in one day.
You just went on and there was more and more, and all of these bodies grouped together, the ages between 18 and 35.
Men, shots to the head.
I mean, this whole thing was-- how do you explain all this?
The only way to explain it was the conflict.
These were the victims of the enforced [indistinct]. Narrator: The records of anonymous corpses led investigators to nearby pits, where generations of the poor had been discarded.
The next task was exhumation, which required investigators to rappel through 75 feet of darkness to reach the corpses at base.
Stover: What the perpetrators wanted to do was remove certain people out of the communities because they may be organizing in ways that they''re not happy with.
And so, I don''t care if it''s in Zimbabwe or it''s in the former Yugoslavia, if it''s in Bosnia or Rwanda or Argentina or Guatemala, the modus operandi is basically the same, and that is to capture people, take them, and execute them away from any witnesses, and then to bury them anonymously and hope that no one ever finds them.
Narrator: The remains were not only anonymous, they were also intermingled and decayed.
The foundation urged relatives of the disappeared to provide DNA samples which would speed identification.
[Speaking Spanish] Narrator: Aquiles Morales lost not only his activist brother Sergio.
Fully 16 members of their labor rights group vanished without a trace.
[Speaking native language] Ha ha!
Narrator: The discovery of remains at La Verbena led human rights investigators to expand their search for the missing.
Peccerelli: Next step was extremely logical.
We targeted military installations because the military had lists of these internal enemies of the state.
So, we thought there''s a lot of bodies in these places.
Narrator: Their hunch proved correct.
Investigators have discovered hundreds of bodies at military and national police bases.
Although the military installations represent 2% of our investigations, we''ve recovered 21% of the bodies in these military installations.
Narrator: In addition to bodies, investigators have also discovered secret government archives containing records of police and military operations.
Among the most significant finds was a military diary nicknamed 'The Death Squad Dossier.'
Military diary is a document that was smuggled out of a military archive and is given to Kate Doyle of the National Security Archives in the States.
It shows how the military documented internal enemies of the state, and among that is 183 people, documented, with pictures and descriptions.
Nicknames, organizations they belong to, salaries, locations where they were captured, and sometimes, the date when they were executed.
Narrator: Among the victims identified in the death dossier is Sergio Saul Linares Morales.
His photograph appears alongside dates of his capture and execution.
Using DNA analysis, the foundation identified Sergio Morales'' remains among corpses exhumed at a rural military base.
Instead of burying the body, the Morales family donated Sergio''s remains to the foundation, which now showcases them in a case outside its laboratory.
Narrator: The process of determining historical truth formally began in the mid-1990s when the civil war ended.
Memorials were erected to the victims and as a condition of the peace accord, Guatemala established a historical clarification commission to detail the fate of the disappeared and massacre victims.
The commission''s final report, entitled 'The Memory of Silence,' was presented in 1999.
Doyle: The commission was willing to articulate the intentionality on the part of the government that these were deliberate operations that were intended to kill civilians.
[Man speaking Spanish] [Applause] Doyle: The commission called out the Army over and over again for the atrocities it committed.
You couldn''t say this in any more kind of powerful, succinct way.
Narrator: The truth commission determined that state-sponsored terror peaked in the early 1980s during the reign of a general named Jose Efrain Rios Montt.
Under his command, the Army embarked on campaigns of genocide and annihilation in indigenous villages.
Fully 80% of the crimes were committed during Montt''s dictatorship.
[Woman speaking Spanish] Narrator: Claudia Paz y Paz was appointed Attorney General of Guatemala in 2010, part of a new wave of reformers in a country long ruled by the military.
Shortly after her appointment, she began exploring indictments for perpetrators of crimes cited in the truth commission report.
[Chanting in Spanish] Narrator: With indigenous people and international human rights groups expanding their protests against impunity, Paz y Paz charged former President Rios Montt with genocide and crimes against humanity.
Narrator: The most incriminating evidence was this log book for one Operacion Sofia, which an anonymous source leaked to Kate Doyle.
The acts of genocide against Mayan communities detailed in these pages were executed by senior officers.
Doyle: What''s amazing about the Operacion Sofia records is that you get the orders, you get the plan, you get the commander''s orders, and then you get the reports from the field from those patrol units that go back to the commanders and then back up to the top.
Narrator: At the top of the Operacion Sofia command structure, Guatemala''s then-leader, General Efrain Rios Montt.
In 2013, he was tried in Guatemala state court for the genocide of 1,700 Mayan Ixils.
[Speaking Spanish] They had almost 100 witnesses-- people who had seen the massacres, people whose family members died, people who were personally raped.
They came for this and they spoke honestly, openly, in their own language, in the Ixil, and Rios Montt had to listen with headphones to their stories.
Narrator: On May 10, 2013, Rios Montt was convicted on all charges of genocide and crimes against humanity.
[Speaking Spanish] [Crowd cheering] Narrator: But 10 days later, Montt appeared in the constitutional court to hear that his conviction had been annulled.
Other reversals quickly followed.
Claudia Paz y Paz was removed from office along with her prosecutors and judges who had convicted Rios Montt.
Narrator: Rios Montt will face a new trial in 2017, but his health is failing.
The constitutional court declared that in the event of a guilty verdict, he will not be imprisoned.
The legal reversal has not deterred human rights investigators.
Human remains continue to arrive at the foundation, and international activists continue to amass evidence of the crimes.
Peccerelli: This work has nothing to do with the dead.
It has everything to do with the living and the damage that that missing person causes to the people that were able to survive these horrible ordeals.
Doyle: I think Guatemala has taught us that the road to accountability, justice, truth, maybe even reconciliation is a very long and treacherous road, and there are people in those societies that are willing to travel it for their entire lives.
Announcer: Next time, Bosnia, Rwanda, Eastern Congo.
Modern warfare requires modern courts.
Man: The tribunal was set up and it seemed to be something that was without precedent.
Announcer: But are these trials justice?
We need to create a system where the communities in which this happened are the communities that account for it.
Ryan: The courts are there. Whether justice is being done, though, is a separate question.
Announcer: 'Dead Reckoning: In Our Time.'
'Dead Reckoning' is available on DVD.
The companion book for this episode, 'Hiding in Plain Sight,' is also available.
To order, visit shoppbs.org or call 1-800-PLAY-PBS.