In the evening hours of a sweltering Friday at the end of April, a team of U.N. lawyers in Cambodia alerted Secretary-General Ban Ki-moon to a crisis at a tribunal built to serve the millions of victims of the Khmer Rouge, arguably the most important court functioning in the world today.

That day, the lawyers’ bosses — a judge from Germany and a prominent Cambodian appeals judge — had shut down an investigation of two Khmer Rouge military leaders for war crimes and crimes against humanity before it had even really begun.

“It is our duty to notify you that we consider, as a matter of law and procedure, that the co-investigating judges did not conduct a genuine, impartial or effective investigation and as such did not discharge their legal obligation to ascertain the truth,” the lawyers wrote. “In our view, the decision to close the investigation at this stage breaches international standards of justice, fairness and due process of law.”

The families of countless victims in the case would be denied justice. The leaders of Pol Pot’s navy and air force — accused among other crimes of eliminating more than 4,500 of their subordinates — would never be held to account for their alleged involvement in torture, executions and forced labor.

And this would undoubtedly appear to have been done under pressure from the Cambodian government, which had publicly announced that the case, as well as another larger investigation, was not “allowed.”

The team told Ban that it was writing “to seek your guidance on how to proceed in these circumstances.”

In the seven months since the letter was written, the United Nations has not offered a substantive answer to these problems. Indeed, as matters continued to worsen, officials at headquarters in New York determined that their hands were tied, leaving matters to deteriorate to the point of scandal.

It wasn’t supposed to be this way. In 2006, the United Nations and the Cambodian government jointly established the court, known officially as the Extraordinary Chambers in the Courts of Cambodia, to deliver justice for the crimes of a regime that had left up to 2.2 million Cambodians dead between 1975 and 1979 and devastated an entire nation. The trials were to consider the greatest number of victims of any since Nuremberg, a half century earlier.

Opening arguments began on Nov. 21 in the court’s second case, a landmark of international law involving senior leaders of the former regime charged with crimes against humanity, genocide and war crimes for their alleged roles in a revolution that caused mass movements of millions of people at gunpoint, enslaving virtually all Cambodians in a regime of forced labor, imprisonment, hunger, torture and execution. Only three accused are likely to stand trial, as trial judges declared that a fourth defendant, former Social Action Minister Ieng Thirith, is mentally unfit (though prosecutors are appealing).

The leader of Pol Pot’s secret police, Kaing Guek Eav, alias Duch, was convicted in 2010 in the court’s first case of crimes against humanity, for overseeing the brutal extermination of an estimated 14,000 people.

But as the court came to two other politically sensitive cases at the end of last year, Dr. Siegfried Blunk, hand-picked by the United Nations to serve as one of two co-investigating judges, began a crude attempt to whitewash five suspects accused in the deaths of hundreds of thousands of people, including immediately telling his staff to seek new employment and that their office would likely close by the end of 2011.

In addition to the case closed in April, Blunk all but publicly announced his intention to dismiss a fourth case in which prosecutors said three mid-level officials were tasked with a wave of criminality that swept Cambodia in 1977 as the regime began to falter, resulting in forced labor, genocide and an estimated number of executions that added up to between 250,000 and 300,000 people killed.

Blunk remained equally opposed to a thorough investigation in this case, too, confining his inquiries to a handful of witnesses per suspect, whom he interviewed personally instead of delegating this task to investigators, and taking the unusual step of using the world “insolent” twice in a confidential order refusing a request from U.N. prosecutors to put evidence on file. One witness interviewed by Blunk described conditions that appeared less than likely to elicit candor — he was conspicuously summoned to testify in front of local government officials and denied knowledge of any crimes, before changing his story when private researchers visited him later.

Blunk resigned in October this year amid calls for an investigation into allegations of his own misconduct. Judge Laurent Kasper-Ansermet, a Swiss financial crimes investigator, is now preparing to take office as his replacement. But he inherits an office now deserted by its legal staff and a situation in which all sides have dug in their heels for more than three years.

Court officials and observers say that, rather than strengthening the rule of law and holding the Khmer Rouge accountable for their crimes, the U.N.-sponsored effort has risked reinforcing the notion that powerful people can dictate the law. “This is the worst possible example that we can set here. If you have the right judge, you can secure impunity,” a U.N. staff member who worked under Blunk told me. “We came here to do exactly the opposite.”

“No one believed what we were saying … until the whole thing blew up.”

Blunk, by the accounts of some who have interacted with him, is a bizarre man. Upon taking office in December 2010, he refused requests for interviews and quickly recalled his investigators from the field. On Dec. 16, he wrote a rambling letter to billionaire philanthropist George Soros, the founder of the Open Society Foundations, complaining of the “insolence” of its subsidiary Open Society Justice Initiative (OSJI), which monitors the court, and threatening to denounce Soros publicly.

“One of your female staff recently tried to invite me by e-mail ‘for breakfast’ at the luxury hotel Raffles Le Royal. Is this the kind of ‘technical assistance’ you envisaged?” he wrote. “I would appreciate a timely answer to these troubling questions to avoid going public on them.”

Aryeh Neier, president of the Open Society Foundations and chair of OSJI’s board, responded by calling the letter’s claims “not well considered.”

Reached by telephone, Blunk hung up on this reporter. According to the contents of official records and allegations made in interviews with senior court employees, in his 10 months on the job, he deliberately avoided collecting information, distorted the law, and repeatedly threatened his own staff, the news media, the chief U.N. prosecutor and anyone else who got in his way with disciplinary measures and even criminal sanctions.

On his arrival, he told his office that his inquiries would be “suspect-based,” seeking first to determine the guilt or innocence of defendants before examining the facts and allegations, a backwards approach his staff said appeared designed either for a frame-up or a cover-up. The method would be as if, upon discovering a dead body, police in a small town first attempted to clear a bystander of murder before even determining the cause of death.

Blunk’s decision to close the investigation into the Khmer Rouge military came immediately after hearing damning evidence. On April 27, two days before he closed the investigation, Blunk and his Cambodian counterpart Co-Investigating Judge You Bunleng heard their last witness in the case — Duch, the convicted former leader of the secret police.

The suspects in the military case, known officially as Case 003, were Sou Met and Meas Muth, the leaders of the Khmer Rouge air force and navy, who stood accused, among other crimes, of sending thousands of their subordinates to die as suspected subversives at the hands of the secret police at their headquarters in Phnom Penh.

No one alive could have been better placed to provide the information Duch was asked to give, and, though speaking cautiously, he quickly implicated both Met and Muth in the military purge with the late Defense Minister Son Sen, who himself was murdered 14 years ago.

“Before making any decisions, Son Sen always asked for comments and assistance from the heads of the divisions,” said Duch, according to a confidential record of the interview. The remark clearly indicated that Met and Muth would, as a matter of routine, have been consulted throughout the period of arrests and executions, even though he knew of no documentation proving this.

Division secretaries such as Met and Muth also had the power to spare lives, said Duch. But, he said, they “bore responsibility” in the eyes of their superiors for making any such requests.

Rather than pursue these inviting comments, the judges abruptly ended the interview. Blunk and Bunleng ended their investigation in the next 48 hours — at 4:49 pm, the close of business before a holiday weekend.

The case had hardly been touched: Only 20 witnesses had been interviewed. The suspects had not even been questioned.

The next working day, Blunk received an email that sent shudders through his office. Ysa Osman, a Muslim member of the Cham ethnic minority whose suffering was among the worst of all ethnic groups under the Khmer Rouge.

“I feel extremely sad after learning that you have concluded investigations on the Case 003. Last night I tried to close my eyes and forget about it so I could sleep well. But how hard I tried, how suffer I endured in heart,” wrote Osman, who worked as an analyst in Blunk’s office.

“For myself, I still remember very well on the day that my little sister was crying for food until she died,” he wrote. “After arrival at a hospital, she was taken to a morgue while she was still alive. My mother and I followed her to sleep in the morgue with many dead bodies around us. Until morning, the sister died without having a bite of food. Then, some people came to take her body. They threw it on a truck, and drove away.”

According to staff members, Judge Blunk replied by saying that he had been too busy dealing with disloyal subordinates to read Osman’s email, but warned him of sanctions if he communicated with other colleagues in his office.

By May, the court’s staff began to quit. Two days after Osman’s email, Dr. Stephen Heder, a consultant widely viewed as an unparalleled historian of the Khmer Rouge, resigned, citing in his parting email to Blunk a “toxic atmosphere of mutual mistrust generated by your management of what is now a professionally dysfunctional office.”

In early June, members of the legal team began to walk off the job, believing their position had become untenable. The team had been told in late May by U.N. headquarters that, following their letter to Ban, Blunk had himself written to New York, accusing his own staff of interference with the administration of justice — a crime in many jurisdictions — and asking for their dismissals for disloyalty, according to people with knowledge of the matter.

When the departures became public in the middle of that month, judges responded by announcing that the lawyers would be replaced with consultants. But the consultants too began to leave: Amy Eussen, a lawyer formerly of the Yugoslav Tribunal at The Hague, departed after less than a month.

Blunk justified his resignation in October by claiming that public remarks by Cambodian officials who were opposed to the cases under his review had made his work impossible. But U.N. officials in Cambodia claim that his resignation actually arose from his own dirty secrets — that he had been investigated by his own staff and confronted in the final days with evidence of his own alleged misdeeds, and that his resignation almost immediately followed those allegations.

According to two officials briefed on the matter, Blunk and Bunleng began an inquiry in mid-September for contempt of court after the Documentation Center of Cambodia, a repository of Khmer Rouge archives and research, revealed that it had interviewed a witness who had previously been questioned by Blunk at the scene of a former labor camp in western Banteay Meanchey province.

While the precise motives for such an inquiry are unclear, police investigators assigned to the task turned the inquiry on Blunk himself, allegedly uncovering indications of the falsification of evidence, including witness tampering, and the back-dating of orders, according to people briefed on the matter.

“People would go out and interview people and then the rogatory letter is issued,” said a U.N. official describing the findings of the police working against Blunk. A rogatory letter is a document empowering investigators to collect evidence. Issuing it after an interview could make it appear that a witness had been interviewed with prior authorization when in fact this had not been the case — perhaps offering the judges the chance to pick and choose which testimony to enter into the record and which to ignore.

Such a practice would appear to jibe with a minority opinion produced last month by U.N. pretrial judges at the tribunal, which found that Blunk and Bunleng had secretly removed an order from the court’s case file and replaced it with a corrected, back-dated version in rejecting a motion filed by a New Zealander seeking reparations for the death of his brother. According to the pre-trial judges, this hid the fact that they had rejected the request while apparently considering the wrong case.

The minority opinion, which was unsurprisingly opposed by the three Cambodian judges on the pretrial bench, was the first occasion when allegations of impropriety against Blunk and Bunleng became part of the official public record. The ruling clearly made an impression at U.N. headquarters in New York, where a spokesman said that U.N. legal officers would consider the minority opinion and “consult and consider carefully with senior colleagues here at Headquarters about any appropriate future steps.”

What motivated Blunk remains a mystery. In an unprompted denial, the United Nations volunteered in June, months before his resignation, that the judge had not been instructed to scuttle his own cases. But whatever the case, Blunk’s actions seem to fit with the Cambodian government’s desire to sweep Met and Muth’s case under the rug.

It is a desire the U.N. secretary-general should understand quite well, because he was met with a rude shock when he went to Phnom Penh to visit the tribunal at the end of October 2010. After Ban’s private meeting with Prime Minister Hun Sen, who himself defected from the Khmer Rouge in 1977, Cambodian Foreign Minister Hor Namhong announced to waiting reporters that the prime minister had definitively refused to allow the court to expand its prosecutions beyond the two cases already underway.

“Successful convictions will finish with case two,” Namhong declared.

The court’s Cambodian judges and prosecutors, who are more numerous but whose votes are given less weight in deliberations, have sided with this view at every opportunity.

Hun Sen, who rose to power on the back of a Vietnamese military intervention in 1979 that toppled the Khmer Rouge government, has been a vocal opponent of trying more than a handful of Khmer Rouge suspects since at least 1999. He made his first and loudest public objections to the new cases in March 2009, when the taking of evidence began in the court’s first trial.

“I will allow this court to fail but I will not allow Cambodia to have another war,” he said, claiming that if more than a handful of suspects were tried, the country could return to the civil war that had ended by 1998. “This is an absolute stand. Please prosecute only those people,” he said, referring to the five defendants already in detention.

Hun Sen loudly repeated such statements throughout the following years, even expressing displeasure with a Japanese donation because it could allow the court to continue functioning. U.N. officials in New York made no response to his outbursts — a stance that only changed in October when U.N. legal counsel and Undersecretary General for Legal Affairs Patricia O’Brien traveled to Phnom Penh and for the first time “strongly urged” Cambodian authorities not to make such remarks.

The reasons for the Cambodian government’s objections to the additional cases are open to interpretation. A possible motive is that members of Cambodia’s governing class once occupied positions under the Khmer Rouge that are of similar rank to those under suspicion of crimes, making the prospect of broader prosecutions an embarrassment that threatens party unity.

Following his meeting with Hun Sen, according to U.N. officials briefed on the visit, Ban retired to a hotel where he gathered with a small group of people in his delegation, including O’Brien. At one point in the conversation, O’Brien floated the idea of convening a conclave of the tribunal’s judges, who she imagined could unanimously do away with the two cases that Hun Sen did not want.

This idea apparently went nowhere. Clint Williamson, the American prosecutor appointed as Ban’s advisor on the court, revealed on multiple occasions during discussions with tribunal officials that he and perhaps others had likewise considered (but rejected) the possibility of negotiating a political settlement with Cambodian authorities to do away with the unwanted cases.

“It’s really only with the wisdom of hindsight that we can now say, unpalatable as it is, it’s a million miles better than what we have got now” said a court official, who claimed that Williamson, who stepped down in September, had passed on this information, albeit disapprovingly.

Through a U.N. spokesman, the Office of Legal Affairs said it could not discuss the contents of O’Brien’s consultations with Ban, but said there was “never any negotiation with the Cambodian government or any other person or entity concerning the termination of cases 003 and 004.” Williamson did not respond to a request for comment on the matter.

In public, U.N. officials insisted that the court was independent and rejected “media speculation” that Blunk was biased — a posture that appeared to transfer blame from the Cambodian government to expressions of concern from the public and news media. Privately, they decided they could do nothing even if they wanted to.

On June 22, O’Brien, the U.N. legal counsel, replied on Ban’s behalf to the lawyers’ emergency letter to headquarters.

Due to judicial confidentiality, the letters’ authors had themselves declined to elaborate on their circumstances when New York sent emissaries to Phnom Penh in May to examine the matter, she noted. The lawyers’ complaints could not be separated from matters “that are currently or can be anticipated to be sub-judice.” According to O’Brien, the United Nations simply could not touch a pending case.

“[T]he United Nations believes that its commitment to non-interference with the judicial process requires that we refrain from intervening in the matter at this stage,” wrote O’Brien. Grave as their problems might be, they were on their own.

As problems worsened, Cambodia’s allies — the foreign governments who were paying the court’s bills — were no more vocal than the United Nations. A week after Ban’s incident with Hun Sen, US Secretary of State Hillary Clinton visited Cambodia, where a centerpiece of U.S. aid is judicial reform, but avoided directly addressing the controversy. Pressed by a reporter, she said the Cambodian government’s attitude to cases three and four should be subject to consultations with the international community.

“[T]he first piece of business is getting 002 to trial,” she said, referring to the remaining case that is not opposed by the government.

One senior diplomat representing a donor country said that if the cases the government does not like were to be dismissed, those paying the bills would be “relieved.”

“I think there are many people who would actually like cases three and four to go away for a number of reasons,” the diplomat said, citing the cost and length of the trials. “But that doesn’t mean that we are pressuring for that outcome.”

“The whole process is a compromise, and it’s a compromise that the international community knew about from the outset,” the diplomat continued.

The United States in October gave the court’s U.N. side $1.65 million, part of $5 million allocated for the 2012 fiscal year. But the court remains perennially short of cash.

Stephen Rapp, the U.S. ambassador-at-large for war crimes issues, said in an interview last month that the United States had expressed support for the court’s judicial independence but denied that the United States had stayed silent in order to placate the Cambodian government.

Was the U.S. position toward the court affected by the fact that it would be in its “geopolitical advantage” to see cases three and four dropped? “Absolutely not,” said Rapp, who previously served as chief prosecutor at the Special Court for Sierra Leone. “The court has to make its decisions independently on the facts and the law.”

As for whether to support an investigation of the events occurring under Blunk, “we haven’t decided,” he said.

But OSJI, the court monitoring group, believe that the need for such an inquiry is incontrovertible. James Goldston, a former federal prosecutor who serves as OSJI’s executive director, said the current allegations represent “a stain” on the tribunal and “they are potentially a stain on the United Nations and the international community.”

“The goal of an investigation would simply be to establish the truth, to what extent these allegations are founded that the co-investigating judges deliberately shut down the Case 003 investigation without attending to the facts and the evidence,” Goldston said.

Some sectors of the Cambodian public, particularly enclaves of former Khmer Rouge, appear jittery — even baffled — by the prospect of additional Khmer Rouge trials. But a survey by the Documentation Center in 2009 found that 57 percent of Cambodians favored more prosecutions rather than fewer.

For Soeung Lim, a 75-year-old rice farmer and layman at a pagoda in Kampong Cham province’s Prey Chhor district, the court is a far more distant reality than his memories of the murder and madness that once surrounded him.

In an interview at his hut — a stone’s throw from the former Met Sop Security Center, one of the 29 distinct crime scenes identified by U.N. prosecutors in 2009 where executions stretched into the hundreds of thousands — he recounted the atrocities of Khmer Rouge rule. “They killed children like they killed a frog. They killed like a beast, animals,” he said.

As the court struggles to bring justice to those responsible for these crimes, it comes closer to affirming the Khmer proverb: Omnach khlaing cheang chbab. “Power is stronger than the law.”

This article was reported in partnership with the Investigative Fund of the Nation Institute.