AMY GOODMAN: We turn now to Indonesia, where an estimated 176 million people voted Wednesday in the country’s second direct presidential election since the fall of the Suharto dictatorship over a decade ago. Exit polls suggest the incumbent president, Susilo Bambang Yudhoyono, has a clear lead and may have been re-elected with more than 50 percent of the vote, enough of a margin to avoid a runoff in September.

President Yudhoyono, often simply known as SBY, is a former army general. His running mate Boediono is a former Central Bank governor. His rivals include the current vice president Jusuf Kalla and the opposition leader and former president Megawati Sukarnoputri, the daughter of Indonesia’s first postcolonial president, Sukarno. Both Kalla’s and Sukarnoputri’s running mates are former generals accused of atrocities during Suharto’s rule. Unofficial count shows Sukarnoputri with 27 percent of the vote and Kalla with 15 percent.

In an article published Tuesday, the New York Times describes incumbent President Yudhoyono as the, quote, “cleanest of the candidates.” But documents recently declassified by the State Department tell a different story. The documents implicate him in the cover-up of the Indonesian military’s role in the August 2002 murders of two Americans and an Indonesian in West Papua. The documents were obtained through a Freedom of Information Act request and released online last week. They show that Yudhoyono first stalled an FBI investigation and then, when agents were finally allowed into the country, limited the scope of their work. Back in 2003 the US ambassador to Indonesia called the murders the, quote, “most important issue in the bilateral relationship.”

Well, earlier this year, Secretary of State Hillary Clinton traveled to Indonesia and praised the country’s democratic transformation, calling for a, quote, “comprehensive partnership” between the US and Indonesia.

HILLARY CLINTON: You know, the United States and Indonesia share more than interests; we do share common values. We have both embraced democracy. Indonesia has experienced a great transformation in the past ten years, building strong and growing institutions, welcoming and developing a vibrant civil society, and, at the same time, respecting human rights in a successful fight against terrorism and extremism.

AMY GOODMAN: Secretary of State Hillary Clinton on improving ties with Indonesia.

I’m joined now by three guests.

Paula Makabory is a Papuan human rights activist. She worked with the Indonesian police in FBI investigations into the 2002 murders. She now lives in exile in Australia. This is a Democracy Now! exclusive, as she speaks out on the investigations for the first time. She’ll join us on the phone from Melbourne, Australia. We’re also joined by Eben Kirksey in San Francisco. He’s a postdoctoral fellow at the University of California, Santa Cruz, and the author of an extensive article tying the 2002 murders in Papua to the Indonesian military. He released the latest documents online last week, along with John Miller, the national coordinator of the East Timor and Indonesia Action Network, who also joins us here in our firehouse studio in New York.

I wanted to begin, Eben, with you. Lay out what these documents show that you just got your hands on.

EBEN KIRKSEY: So, these new documents describe the role of President Yudhoyono in this cover-up, as you described in your introduction. There were really two stages to the cover-up. Essentially, the first stage was when Yudhoyono blocked the investigation. At that point, he was the coordinating minister for security and political affairs. While he was, you know, stalling, basically there were military agents on the ground in West Papua systematically intimidating witnesses, also tampering with the crime scene. By the time the FBI investigators got there — this is January 2003 — basically the scene — the trail was cold.

And at the next stage, basically in a pretty rare move, you know, for someone of his stature, he micromanaged the investigation. He met repeatedly with these low-level employees of the US government, FBI investigators, and sort of defined the terms of their investigation, determined who they were able to meet with. Initially, these FBI investigators had very limited access to material evidence, as well as witnesses. During a lot of their interviews, basically they had Indonesian military agents, minders, sitting in on the interviews with them. So, from the outset, really, the investigation was compromised.

AMY GOODMAN: And, Eben Kirksey, tell us who the murder victims were. Why were they in West Papua?

EBEN KIRKSEY: They were American schoolteachers. They were contract employees for Freeport McMoRan, a US gold mining company. It’s one of the largest gold mines in the world. They also have copper there. Basically, the teachers were on a picnic They were traveling along this mountain road, one of the most heavily guarded roads in Indonesia. And about 300 yards from a checkpoint, an ambush began. They were pinned in their cars for about forty-five minutes, and two teachers were killed: the school’s president, Ted Burgon, as — sorry, the school’s principal, Ted Burgon, as well as Rick Spier. There was also an Indonesian teacher killed, Bambang Riwanto.

AMY GOODMAN: And why were they targeted, do you think?

EBEN KIRKSEY: So, one possibility is that the Indonesian military was looking for more money. In that year, 2002, Freeport paid $5.6 million to the Indonesian military for protecting their mine. In addition to that lump-sum payment, there was a payment of about $46,000 to a Kopassus officer. Kopassus, they’re the special forces of Indonesia. This Kopassus officer was placed at the crime scene by witnesses. So, in short, the motive appears to be trying to get more money.

AMY GOODMAN: And these are US citizens, two of — there were three people, US citizen, as well as an Indonesian teacher killed?

EBEN KIRKSEY: Right, two US citizens, one Indonesian was killed. There was eleven others wounded.

AMY GOODMAN: The US ambassador, again, to Indonesia, saying this is the most critical issue for the US-Indonesia relationship? When did he say that? And how did this change?

EBEN KIRKSEY: Basically, you know, initially it seemed that the Bush administration was going to completely ignore what happened. One of the widows of this attack, the widow of Rick Spier — her name is Patsy Spier — launched a very effective campaign, and Congress got involved. So, basically, military aid to Indonesia became conditional on the outcome of this investigation, you know.

And it became very clear that high-level Bush administration officials took an interest. So, for example, during the confirmation hearing of Condoleezza Rice, there was this Q-and-A session, and Senator Biden — then senator, now vice president — asked her about the case. Basically, Clinton said that — or, sorry, Rice said that there was no evidence of Indonesian military involvement. At the same moment, Rice said that it was an imperative to work with the Indonesian military.

So, basically, you know, there was a high-level initiative by the US government, also involving figures like Robert Zoellick, current World Bank president. He traveled to Jakarta in May 2005 and reiterated that same message, that there was no evidence of Indonesian military involvement in this attack, when, in fact, there was a lot of very specific evidence tying the military.

That Kopassus officer that I mentioned earlier was placed at the crime scene by witnesses. We have ballistics evidence suggesting that there were a number of shooters, in addition to the people who were eventually put into prison. The FBI was given lots of very, very specific information linking the military to this attack. And, you know, they basically failed to systematically pursue and develop these lines of evidence that would have pointed to the military culprits.

AMY GOODMAN: I wanted to bring Paula Makabory into this conversation, the Papuan activist with the Institute of Papuan Advocacy and Human Rights. Can you talk about the investigation? You worked closely with the Indonesian police investigators, as well as the FBI. You’re speaking out on this now for the first time in exile in Australia. Tell us what happened.

PAULA MAKABORY: Yeah, truly, I was involved with the investigations in the first year and the second. And then, we knew that the attitude in the [inaudible] is changing and then look like now who is there in that [inaudible] those civilians. So, I worked closely with the police team in the other side, like because he was close to the local people. And then we got information that actually those Kopassus members already take place before these groups went there. And then it seems like the police — the police preliminary investigations, it lacked our information from the ground, that the executors in the hill is — they’re the military themselves.

Why I say this? Because according to [inaudible] testimony, in the beginning, that on the 28th of August, actually they were there at the crime scene, built up their case, but they also saw those Indonesians Kopassus already took place in a nearby area. It’s two days before the attack. And then again, during the attack, [inaudible] finds that he gets shot, the other part of that — the right side of the vehicle. And then —- and then I believe that after I talked to other persons remember [inaudible] at the same time. They also have different stories on the news.

So, it seems like on the news in the beginning, during the FBI investigations, when I took him to meet them, he also produced two different stories, again and again, that he involved and not involved. And then, during the time FBI asked him who paid him to tell him the story. So I went there to guerrillas’ leaders, to the [inaudible] groups in the jungle, and then I asked them. They, all of them, didn’t know what’s going on up on the hill. And then they say that it is [inaudible] and then who were there. One of the witnesses who already got killed, he witnessed that the other groups were there on the other side. They just shot one. And then they understand that the shooting is what killed anyone. But, and then there is another people from the other side. If you look at the evidence -—

AMY GOODMAN: Paula, can you describe, after working closely with the FBI, when they first came onto the crime scene, what was their line of questioning? And were they looking at Indonesian military being involved in the attack?

PAULA MAKABORY: Yeah, I would like to let the listeners or American citizens know that actually I’m the West Papuan human rights worker who tried to work closely with the FBI and very upset until today, because justice [inaudible] and it’s true that we would like to achieve through these very provisional institutions are far away from what we would like to achieve, because I saw that the FBI failed to get to investigate those Indonesian military officer. I think the Indonesian police have been trying to do their best in the beginning, and we all understand. I am West Papuan. I understand what’s going on in this area.

And then we knew exactly that the Kopassus in that area were informed, if we go through the evidence. You know, FBI, at the time, when he tried to stall the investigations in the first year when the shooting happened, this is — this is [inaudible] the people there in that crowd to remove all that evidence. If the FBI care about justice and about those American teachers, they should be there in the first place, in the first time. But in there, we could see that some of the witnesses being intimidated and terror. Those Indonesians themselves, those drivers who pass by that are there during the attacking. And then, some of the Freeport workers who were on the crime scene at the time is now not working anymore at Freeport.

AMY GOODMAN: Paula, I wanted to go to John Miller, who is national coordinator of the East Timor and Indonesia Action Network. John, the significance of what is being laid out here, of what Paula found working with the FBI and the Indonesian police, as well as this implicating Yudhoyono, the man who could well be elected president today, as the results come in, of Indonesia?

JOHN MILLER: Well, at the time these killings happened, the US was moving to restore the military relationship with Indonesia that had been cut off in the aftermath of the violence in East Timor in 1999.

AMY GOODMAN: When East Timor voted for its freedom.

JOHN MILLER: Voted for independence and the country was destroyed for its trouble.

AMY GOODMAN: The Indonesian military burned it to the ground —

JOHN MILLER: Right, militia and –

AMY GOODMAN: — as the people of Timor voted.

JOHN MILLER: Directed by one of the vice-presidential candidates, General Wiranto. And this became a snag, a roadblock, in that effort. So the more that could be done on the Indonesian and US side to disassociate the Indonesian military from these killings, the hope was that that would then speed up the effort to particularly restore military training, IMET, which was actually the first thing that was cut off back in the early ’90s after the Santa Cruz massacre in East Timor. And the Indonesian police, as Paula and Eben have said, found that they thought the military was involved. Subsequent investigations have pointed to that, except for any of the official investigations. And it’s not surprising that SBY would be involved in doing damage control for the military.

AMY GOODMAN: SBY, again, the president, Yudhoyono.

JOHN MILLER: Right. And he’s — I mean, I think in his presidency has shown that he’s very uninterested, despite some good human rights rhetoric, in accountability for past human rights crimes that have taken place.

AMY GOODMAN: And tell us who — exactly for what Freeport McMoRan is the significance, of one of the largest gold and copper mining operations in the world, the US multinational.

JOHN MILLER: It’s a New Orleans- and Austin-based corporation. It’s a US company. It was one of the first big US multinationals let in by Suharto, the former dictator of Indonesia, after he overthrew Sukarno, the founding president. And it’s one of the biggest income generators for the Indonesian government. And it’s considered by the Papuans a big thorn in their side. It’s environmentally very damaging. They don’t feel they get enough of the money that comes into Indonesia to pay for the gold and the royalties for the resources. And Freeport has, therefore, an inordinate influence on US-Indonesia relationship on both sides.

AMY GOODMAN: Finally, the other candidates — you’ve got Yudhoyono — these documents implicate in the cover-up, and as you were just mentioning, the vice-presidential candidates of the other contenders in today’s election.

JOHN MILLER: OK. Megawati’s vice-presidential candidate is Prabowo, former head of Kopassus Special Forces, probably the worst military unit, among many, in the Indonesian military. He was actually in the aftermath of the overthrow of Suharto. He was — lost the power struggle with Wiranto, the other vice-presidential candidate, and was found to have kidnapped and presumably executed a number of activists, including some from Megawati’s own political party.

AMY GOODMAN: He’s the son-in-law of Suharto?

JOHN MILLER: And he was the son-in-law of Suharto, and has pretty much as admitted his involvement in that. He’s also accused of having engineered the rioting that actually led to Suharto’s overthrow, primarily directed at Chinese Indonesians.

The other vice-presidential candidate is General Wiranto, also former general. He was the defense minister and head of the military in 1999. He was indicted by a UN-backed process in East Timor, an indictment that’s not been followed up on by the UN or on the East Timorese side or by the Indonesians. He was actually recommended for prosecution by Indonesia’s own Human Rights Commission, but the few prosecutions that did take place did not include General Wiranto.

AMY GOODMAN: Final comment, Eben Kirksey, as a cultural anthropologist, as a professor at University of California, Santa Cruz? The significance of these documents that have now been released and what you think needs to happen now?

EBEN KIRKSEY: Well, I think, really, you know, the omissions of the documents are what’s really interesting. There’s a big blank — blank spaces on them. And I invite all the viewers to check them out. They’re published on the internet, both on my blog and on ETAN’s website. If nothing else, you can sort of get the strange jargon of the State Department.

But, you know, the documents are silent on the roles of the Bush administration in this cover-up. And, you know, from the public record, as I was alluding to earlier, there are big names, big players, who have their fingers all over this: Zoellick, Condoleezza Rice — John Ashcroft is a name I haven’t mentioned yet — Robert Mueller. All of these very key figures in the Bush administration were involved.

And I think, at this moment in history, you know, it behooves Congress to open this back up. The FBI investigation is technically still open, so I think Eric Holder’s Department of Justice really needs to move on this, bring it to closure, and really go after the perpetrators.

The impunity in this case, you know, the death of these two Americans, speaks to much broader problems in West Papua right now. In just the last few months, we’ve had seven Papuan woman, for example, kidnapped and raped. We had a thirteen-year-old boy last month who was shot. Scores of Papuans have died in Yudhoyono’s first regime, and I expect the situation on the ground is not going to change, that it’s going to continue to get worse. So, you know, I think bringing this case to closure will both protect the human rights of Americans abroad, but also of Papuans. And there’s really a lot more to say on that, but I’ll leave it there.

AMY GOODMAN: Eben Kirksey, I want to thank you for being with us, from University of California, Santa Cruz, speaking to us from Link TV’s studios in San Francisco. We will link to your article. Paula Makabory, thank you for joining us, Papuan activist with the Institute of Papuan Advocacy and Human Rights. And John Miller, national coordinator of the East Timor and Indonesia Action Network, headed to East Timor in August for the tenth anniversary of the historic referendum, where Timorese went to the polls and voted for their freedom from the Indonesian military.