BANGKOK, Thailand — It was only two months before the 2003 Asia-Pacific Economic Cooperation (APEC) meeting in Bangkok — President Bush would be attending — and Thai soldiers and police had the building surrounded. Their mission: to nab one of the world’s most wanted terror suspects, the man thought to be one of the masterminds behind the spectacular nightclub bombings in Bali that had killed more than 200 people a year earlier.

The operation, in Ayutthaya, a sleepy city north of Bangkok, went off without a hitch. A soldier kicked down the door and others stormed in. The suspect, Riduan Isamuddin, an Indonesian national better known as Hambali, had been on the run since the Bali bombings. He was captured without any serious resistance and whisked away without a trace, save for an old passport photograph authorities provided to the press depicting a bespectacled man with a slightly pudgy face. It was August 11, 2003, and the next time Hambali’s whereabouts would be known would be more than three years later, when President Bush listed him as one of 14 key prisoners moved from secret CIA prisons to the United States naval base at Guantánamo Bay, Cuba.

Then-Thai Prime Minister Thaksin Shinawatra asserted that Hambali had been planning an attack that could upstage even the Bali carnage: a bomb attack on the upcoming APEC meeting. Three days after the arrest, President Bush declared that Hambali was “no longer a problem to those who love freedom” and when he was in Bangkok for the APEC meeting Bush warmly referred to Police Maj.-Gen. Tritos Ranaridhvichai, the Thai police officer who was officially responsible for the arrest, as “my hero.”

But the arrest was more than just a Thai operation — the U.S. Central Intelligence Agency had set it up. Within days its agents took the captured Hambali away in a technique that has come to be known as an “extraordinary rendition” — the transfer, outside of any legal process, of a terrorist suspect to a foreign country for interrogation that human rights activists contend often includes torture. The fact that the CIA was allowed to plan and lead such a secret operation in Thailand was only one of the ways the country has shown itself to be a strong ally of United States in its pursuit of terrorists — once Thaksin was persuaded to stop distancing himself from the U.S. invasion of Iraq.

“President Bush needed to show the world that the U.S. was not alone in its anti-terrorism war,” said Matthew Wheeler of Chulalongkorn University’s Institute of Security and International Studies in Bangkok and a former counterterrorism analyst with the U.S. think-tank Rand Corporation. “He needed cheerleaders.”

Thaksin did not rush to claim the cheerleader role. In April 2003, The Asian Wall Street Journalreported that Thailand was on the list of countries likely to be “punished” by Washington for not giving enough support to the war in Iraq. Two months later Thaksin went to Washington for a personal meeting with President Bush. He emerged with his new role and benefits for Thailand — some of which came at an unexpectedly high price:

  • In a major symbolic gesture, President Bush suggested that Thailand could become a Major Non-NATO Ally. The designation in fact occurred that October, upgrading Thailand to the level of America’s key strategic allies in Asia alongside the Philippines, South Korea, Japan, New Zealand and Australia; benefits include credit guarantees for major weapons purchases and priority access to used U.S. military hardware. Political opponents assailed Prime Minister Thaksin as a U.S. “yes-man,” drawing comparisons to the much-hated military dictators of the Vietnam War era.
  • The U.S. increased military aid, providing $4 million in Foreign Military Financing in the three years after September 11, 2001, where there had been none before; $1 million from the new Regional Defense Counterterrorism Fellowship Program from 2002 through 2005; and an increase in money for fighting Thailand’s major narcotics trade — the country includes part of the Golden Triangle opium poppy region — from roughly $18 million in the three years preceding 9/11 to more than $23 million in the three years after the attacks.
  • Thailand sent a battalion of army engineers and medical staff to Iraq in 2003 to join the U.S.-led “coalition of the willing,” but political opposition swelled after two Thais were killed and the troops were brought home about a year later.
  • President Bush promised economic concessions including negotiations on a free trade agreement with Thailand. Negotiations began in June 2004 but foundered after political opponents inspired public protests.
  • Thailand also acceded to a U.S. request to exempt its citizens in Thailand from prosecution in the International Criminal Court. The Bush administration is campaigning for such exemptions for fear that politically motivated charges could be brought against U.S. soldiers and officials.
  • The U.S. began turning a blind eye to human rights abuses, including some carried out by Thai government security forces against Muslims in Thailand’s southern provinces, where a renewed insurgency has killed hundreds and where three community leaders were arrested and later acquitted. Anti-U.S. sentiment among Thai Muslims is strong.

All of these developments have stirred the volatile politics of Thailand, a predominantly Buddhist country of 65 million that has long drawn a wary eye from human rights organizations. In September 2006, the elected government fell once again to a military coup. Since the coup, the U.S. has cut off military aid and assistance to the country.

The Thai military cited two primary justifications for the coup d’état: a number of high-profile corruption cases against members of Thaksin’s cabinet and family, as well as what it characterized as Thaksin’s attempt to undermine the authority of the Thai king, a highly respected figure. Military leaders did not cite Thaksin’s deal with the Bush administration as a reason for launching the coup.

Despite Washington’s cutoff of military aid, the recently installed prime minister, Gen. Surayud Chulanont, expressed confidence in the U.S.-Thai relationship after meeting with President Bush at the 2006 Asia-Pacific Economic Cooperation summit in Hanoi, Vietnam. According to Surayud, Bush thanked him for his explanation of political developments in Thailand. A security source in Bangkok told the International Consortium of Investigative Journalists (ICIJ) that a number of coup leaders had fostered strong ties with the U.S. as they came from the ranks of the Thai special forces, a military unit with a history of close relationships with the U.S.

Traces of a center

Without Hambali’s horrific reputation, his arrest would have seemed less dramatic. Intelligence agencies identified him as a top leader of Jemaah Islamiyah (JI), an Indonesian-based organization believed to have a strong connection with Osama bin Laden’s al Qaeda, and said he had been trained in Afghanistan and involved with a string of terrorist attacks in Southeast Asia, mostly in Indonesia. He was also on the Interpol “red notice” list, a category for the world’s most wanted criminal fugitives, on a request from the Indonesian police. The CIA has called him “the Osama bin Laden” of Southeast Asia.

Thai military and police sources told ICIJ that Hambali was whisked from Ayutthaya and flown out of Thailand on an American military plane. In December 2005, Human Rights Watch listed Hambali among the “ghost prisoners” being held in unknown locations. In September 2006, Hambali arrived at Guantánamo Bay.

A Thai intelligence source told ICIJ there was no legal justification for removing Hambali from Thailand after his arrest. “No charges were pressed against Hambali,” the source said. “The Thai legal system says any person arrested in Thailand must be charged and sent to court here. Also, all criminal arrests must be done by the police, not the military. The Hambali arrest was actually led by the military.”

But according to Gen. Chavalit Yongchaiyudh, the former Thai prime minister who became deputy prime minister under the Thaksin government, the operation to capture Hambali was really led by the CIA. “The Hambali arrest was an American intelligence work using our hands,” Chavalit told ICIJ in an interview. “They took him away and agreed to send us information they found out from him.” A former Thai intelligence official familiar with the Hambali operation said, “The reason why the Americans asked us to help arrest him was because they had no legal jurisdiction in Thai territory.”

Chavalit said the CIA worked through a top-secret U.S.-Thai intelligence cooperation unit called the CTIC (Counterterrorist Intelligence Center) that was established several months before the 9/11 attacks.

According to several other Thai sources and the Center for Strategic and International Studies (CSIS), a respected U.S. think tank, the center is led by CIA officers and works closely on a daily basis with key personnel from Thailand’s three main security agencies: the National Intelligence Agency, the Thai police and the armed forces. Though based in Thailand, according to a Thai source familiar with CTIC’s operations, it has a network of assets and cooperating agreements with other intelligence services throughout Southeast Asia, assisting their anti-terrorism efforts. According to multiple Thai sources, the CIA provides funding for CTIC although there is no way to determine exactly how much.

According to the former Thai intelligence official under the Thaksin government who spoke on condition of anonymity for fear of retribution, CTIC has no official office. Instead, CTIC personnel work from a number of “safe houses” in Bangkok. According to the former intelligence official, four or five CIA agents were working at CTIC at any given time. Despite the fact that the unit was cooperating with Thai authorities, Thai intelligence officials did not always know what their American counterparts in CTIC were doing. “Even I, who was always with them during the Hambali arrest, did not know where they took Hambali,” the former intelligence official said.

CTIC had been tracking Hambali and other suspected JI members, and its work also led to the reported arrests of two Malaysian nationals as terror suspects. In July 2003, Mohd Farik bin Amin, known as Zubair, was arrested after a meeting with Hambali. And only hours before Hambali was arrested, his colleague Mohammed Nazir bin Lep, alias Lillie, was also captured. Like Hambali, their whereabouts after the arrests were unknown. In September 2006, media reports indicated that Zubair and Lillie were among 14 high-profile terrorist suspects transferred to Guantánamo Bay. Malaysian Prime Minister Abdullah Ahmad bin Badawi, in response to the report and pressure from human rights groups, demanded from Washington a guarantee for their fair trial. The U.S. government has not released further details of the transferred suspects’ trials.

There has also been backlash from beyond Thailand and a price to pay for CTIC’s secretive activities. The Indonesian government tried to have Hambali extradited to Indonesia to testify against another accused JI leader, Abu Bakar Bashir, who was linked with Hambali to the 2002 Bali bombings. However, the efforts failed and Bashir recently walked away free.

Human rights suffer

While U.S.-Thai counterterrorism cooperation has led to important arrests, it has also negatively impacted human rights in Thailand. Before Thailand became an ally in the war on terror, Washington was more direct in its criticism of Thai forces employing excessive force against civilians, especially in a war on drugs that former Prime Minister Thaksin initiated. But once Bangkok agreed to send troops to Iraq and Afghanistan, American officials became more circumspect in voicing their concerns. Thus the Thaksin government could occasionally use heavy-handed measures to crack down on insurgents in the heavily Muslim southern provinces without worrying much about international political repercussions.

Before Thaksin’s trip to Washington, that was not the case. When he became prime minister in early 2001, Thaksin announced his intention to eliminate all illegal drugs in the country. His administration, through the Interior Ministry, began the campaign by issuing a “blacklist” of influential people in each province suspected of being engaged in the illegal drug trade. A series of arbitrary arrests and extrajudicial killings began shortly thereafter. By the end of April 2003, more than 2,000 people on all sides of the conflict and in different parts of the country had fallen victim to extrajudicial killings.

Washington strongly voiced its concerns. But soon after the June meeting with Thaksin in Washington, Bush softened his tone. In a joint statement issued after their working meeting, the White House said: “President Bush recognized Prime Minister Thaksin’s determination to combat transnational crime in all its forms, including drug trafficking and trafficking in persons. Regarding recent press allegations that Thai security services carried out extrajudicial killings during a counter-narcotics campaign in Thailand, Prime Minister Thaksin stated unequivocally that the Thai government does not tolerate extrajudicial killings and assured President Bush that all allegations regarding killings are being investigated thoroughly.” The shift in tone from earlier blunt criticisms of Bangkok’s heavy-handed tactics was clear.

Further, Thaksin’s government issued two executive decrees shortly after Hambali was arrested that emphasized severe punishment for those convicted of terrorism and loosened policies to make detention without trial easier. That led to more political backlash from civil rights advocates, the media and opposition parliamentarians, all of whom accused the government of creating the new legal authorities to justify Hambali’s extralegal deportation.

The CIA and the South

The unrest in Thailand’s three southern Muslim provinces — Pattani, Yala and Narathiwat — has deep roots, but after Thaksin became Washington’s ally, anti-government and anti-American sentiment increased in the region. Suspicions that the CIA was operating in support of the Thai government’s counterinsurgency efforts in the provinces escalated as well.

A military intelligence official in southern Thailand told ICIJ that one of CTIC’s contact points in the region was a Thai military unit based in the Kor Hong subdistrict in the southern Thai province of Songkhla, an area close to where the government is fighting the Muslim insurgency. Other intelligence sources say the CIA’s intelligence work in Thailand, including in the three southern Muslim provinces, is not done entirely by its own American agents. Instead, the sources say, it is carried out through a strongly established network of local informants and agents.

U.S. Ambassador Ralph Boyce has publicly denied any CIA presence in the southern provinces, but his claim has not proved to be an easy sell. Muslims in the three provinces openly share a strong anti-American sentiment.

“I once met with the U.S. ambassador,” said Ahmad Somboon Bualuang, a retired Muslim lecturer at Prince of Songkhla University and a member of an administrative council in Pattani province. “I told him I believed that behind the deteriorating situation here was the shadow of the Americans.”

Resentment was stirred by the 2003 arrests of three well-respected community leaders — Dr. Waemahadi Wae-dao; Maisuri Haji Abdulloh, the owner of an Islamic school; and Abdulloh’s son Muyahi. The authorities said they were JI members and that another terrorist suspect arrested in Bangkok had linked Wae-dao to plans to bomb five embassies and tourist spots in Bangkok, Pattaya and Phuketo.

Their lawyer, Muslim human rights attorney Somchai Nillapaijit, strongly denied the charges. “They deny doing anything wrong and say they haven’t confessed to the police,” he said at the time of the arrests. “They deny all the charges against them, and they want to testify in court.”

Wae-dao’s arrest came shortly before a decade of relative quiet came to an end. Violence in the area, known for Muslim separatist movements in the 1980s, returned suddenly when a group of unidentified men attacked the Fourth Development Battalion in the Narathiwat province on January 4, 2004. The attackers killed four non-Muslim soldiers and carted away more than 100 weapons. The situation worsened four months later when about 300 militants attacked 12 police and military posts in three southern provinces. The clashes took more than 100 lives, including those of five policemen, and ended with the military firing into a historic mosque where some militants were hiding. A number of random explosions and shootings are also believed to have been the work of Muslim insurgents.

The Thai government launched several initiatives in an attempt to improve relations with local citizens and solve the conflict through peaceful means. But while the central government poured in funds for several large development projects in the region, human rights violations by the authorities against suspected insurgents were also taking place, local Muslims and Buddhists told ICIJ.

Many in the area believe that the authorities are behind the disappearances of suspected insurgents, says Somkiat Juntursima, editor of the Pattani-based Issara News Agency, which has been covering the conflict. Abdul Asis Tade-in, vice president of the Young Muslim Association of Thailand and a member of a special committee to investigate disappearances, said almost 30 had been documented since 2004.

The U.S. expressed concern about heavy-handed measures in an incident in October 2004, when thousands of Muslim demonstrators gathered in front of the Tak Bai district police station in Narathiwat to protest the arrest of six village security guards who were charged with stealing government weapons. It ended with a police crackdown; six protesters were shot and killed and at least 78 detainees died of suffocation after they were tied up and piled on top of one another in military trucks. But Washington was generally silent on a number of other cases, particularly a series of abductions of local Muslim villagers after the 2004 weapons theft — and it was silent when it came to the arrest of Wae-dao and the other community leaders.

The accusations against Wae-dao shocked local Muslims. “Muslims in Narathiwat province loved Dr. Wae-dao for what he had done for the community,” said Wisuth Binlateh, a member of Islamic Committee in Songkhla province. “Nobody believed the accusation against him.”

Even some Thai intelligence officers doubted the circumstances of his arrest. “There was no intelligence information from within Thailand that supported the accusation,” a military intelligence official in the south told ICIJ. “The arrest was based only on information from Singapore.”

A further shock was the abduction of Wae-dao’s attorney, Nillapaijit, in Bangkok in March 2004. He was never seen again. Apart from representing the three detainees, Nillapaijit had been an outspoken advocate against alleged police torture of five suspected insurgents linked to the 2004 weapons theft. Five police officers were eventually arrested and charged with the abduction. One police major was sentenced to three years in prison but planned to appeal; the other four were initially released due to lack of evidence although the prosecution has appealed.

Dr. Wae-dao and his co-defendants were acquitted of all charges. The court said prosecutors failed to produce evidence to support their accusations apart from testimony by a suspected JI member held in custody in Singapore. Moreover, the Department of Special Investigations was found to have fabricated documents that were then introduced as evidence by prosecutors. In April 2006, Wae-dao ran to represent his home province of Narathiwat in the Thai Senate. He was overwhelmingly elected.