Legal teams are interviewing witnesses across the region in preparation for the long-awaited trial of Indonesian terrorist leader Riduan Isanuddin, who has been incarcerated at the United States-run Guantanamo Bay detention facility for 13 years.

Isanuddin, 55, better known as Hambali, was captured by American and Thai intelligence agents in Thailand’s ancient riverside capital of Ayutthaya in August 2003, 10 months after the devastating Bali bombing which he stands accused of funding.

Ironically, the alleged mastermind of the attack will apparently finally go on trial more than a decade after Indonesia and its often criticized judicial system prosecuted the last of the Bali bomb perpetrators, along with 250 other militants linked with the al Qaeda-linked Jemaah Islamiyah regional terror network.

Two US Federal Bureau of Investigation (FBI) agents and two military prosecutors were in Jakarta late last year to gather evidence, and a defense team visited Kuala Lumpur in late June for the same purpose. It is understood some witnesses will be flown to Guantanamo Bay to give testimony in the trial.

But that’s still some months away as US military and civilian judicial authorities continue to wrangle over the nature of the charges to be brought against Isanuddin and his Malaysian associates, Bashir Lap, 43, and Mohammad Farik bin Amin, 44.

In June 2017, a US military court charged Isanuddin alone with the murder of 202 people, 159 of them foreign tourists, who died in the twin nightclub blasts in Bali in 2002. He was also accused of playing a role in the killing of 11 in the 2003 suicide bombing of Jakarta’s JW Marriott Hotel.

Buildings and cars are on fire after a bomb blast in tourist site of Kuta, Bali 13 October 2002. At least 53 people including 10 foreigners, were killed when a bomb exploded in a popular nightclub on the Indonesian resort island of Bali. AFP PHOTO/ DARMA / AFP PHOTO / DARMA
The fiery aftermath of the 2002 Bali bombing that killed 202, mostly foreign nationals. Photo: AFP/Darma

Seven Americans were among those killed in Bali, along with 88 Australians, 38 Indonesians, 23 Britons and nationals from 19 other countries in the worst terrorist outrage since the September 11, 2001 attacks rocked the US.

Over the subsequent two years, the military court’s civilian oversight authority has twice returned the case because of procedural issues, which have never been made clear.

Last April, Pentagon prosecutors refiled the charges, this time including the crime of conspiracy, in addition to the previous counts of murder, terrorism, attempted murder, intentionally causing serious bodily harm and destruction of property as a war crime.

The Pentagon’s Court of Military Commission Review recently declined to rule on whether conspiracy is a lawful war crime, but it still left intact the 2008 conspiracy conviction of Al Hamza a-Bahlul, the sole Guantanamo inmate to be tried so far.

The 49-year-old Yemeni is serving a life sentence for making a recruiting video for al Qaeda and other activities as Osama bin Laden’s media adviser, including setting up a satellite receiver so bin Laden could listen to live radio coverage of the 9/11 attacks.

When a trial for Isanuddin is finally approved, it will be followed by an arraignment before a military commission and then pretrial legal motions. But following proceedings from Indonesia is difficult because the commission’s website is blocked to selected overseas locations for unknown reasons.

New York-based Human Rights Watch contends that the military commissions do not meet international fair-trial standards and should be disbanded, leaving the cases to be adjudicated in US federal courts.

The US flag flies over the war crimes courtroom in Camp Justice at the US Naval Base in Guantanamo Bay, Cuba in a photo reviewed by the US Department of Defense. Photo: AFP/Michelle Shephard/ Toronto Star
The US flag flies over the war crimes courtroom in Camp Justice at the US Naval Base in Guantanamo Bay, Cuba. Photo: AFP/Michelle Shephard

“They (the commissions) are, among other things, mired in excessive secrecy, fail to adequately protect attorney-client privileged communications, and permit the introduction of coerced information,” the organization said in a 2018 update.

Isanuddin’s lawyer, Major James Valentine, told the New York Times recently it would be “a really big stretch” to implicate his client in the Bali plot, noting that a star witness at the trial of the three men later executed for their role in the crime had never mentioned him.

The Pentagon has said it will not seek the death penalty as prosecutors deal with claims that Isanuddin was tortured during the 1,280 days he spent in US Central Intelligence Agency (CIA) custody, mostly at the al-Jafr prison in the desert of southeast Jordan.

Details of his mistreatment there were described in the US Senate Select Committee’s 2014 report into the agency’s worldwide rendition program, whose first victim, Muhammad Saad Iqbal Madni, was secretly whisked out of Jakarta in early 2002.

Madni, 41, was rendered to a similar black site in Egypt and then to Afghanistan’s Bagram airbase before being flown to Guantanamo, where he was held without charge until his repatriation to Pakistan in 2008. His only crime: boasting about his unverified links to al Qaeda.

Like other prisoners subjected to so-called enhanced interrogation techniques, Isanuddin was allegedly waterboarded on numerous occasions at a time when it was deemed as justified by officials in an effort to extract actionable intelligence.

Riduan Isanuddin, alias Hambali, was allegedly tortured during interrogations at a Central Intelligence Agency-run rendition site. Photo: Facebook

To date, all but 40 of the 775 alleged militants detained at Guantanamo since it opened in 2002 have been either transferred to their home countries or released without charge. Many of those remaining are referred to as “forever prisoners.”

Only eight are currently charged with crimes, among them Pakistani Majid Khan, 39, who pleaded guilty in 2012 to delivering US$50,000 from al Qaeda to the Jemaah Islamiyah terror network to fund the 2003 JW Marriott suicide bombing.

The sole legal US resident confined at the Cuba-based facility, Majid has yet to be sentenced and there is speculation a plea deal may see him acting as a key witness in Isanuddin’s trial.

Isanuddin is one of 14 “high-value” detainees confined to a top-secret section known as Camp 7, which also houses al Qaeda mastermind Khalid Sheikh Mohammad, 55, and four others accused of staging the 9/11 attacks.

A federal task force recommended Isanuddin for trial as early as 2010, but nothing more was heard of his case until mid-2016 when the Periodic Review Board said he remained “a significant threat to the security of the United States” in rejecting his request to be released.

Created by the Barack Obama administration to whittle down Guantanamo’s population, the board cited the Indonesian’s role in major attacks and as the key link between al Qaeda and Jemaah Islamiyah as reasons for his eventual prosecution.

It was only in 2008 that Detachment 88 counterterrorism unit officer Tito Karnavian, now Indonesia’s national police chief, and two National Intelligence Agency (BIN) operatives were permitted to interrogate Isanuddin at Guantanamo.

During that questioning, he is said to have made several admissions about his role in the al Qaeda-funded 2000 Christmas bombings across Indonesia, the 2002 Bali bloodshed and the first of the two attacks on the JW Marriott the following year.

The shattered aftermath of the 2003 JW Marriott Hotel bombing in Jakarta. Photo: AFP

But despite pubic statements by some senior officials, Indonesia never pressed the US government to return him to Jakarta for trial, due to worries about the publicity surrounding such a high-profile event and whether his conviction could be guaranteed.

Senior prosecutors said that Indonesia’s 2003 Terrorism Law could only be applied to him in facilitating the transfer of the $50,000 from Khalid Sheikh Mohammad’s nephew, Ammar al-Baluchi, 41, to finance the Marriott bombing of that year.

Mentored by 1993 World Trade Center bomber Ramzi Yousef, 51, the Kuwait-born computer technician also remains in custody at Guantanamo, accused of helping the 9/11 attackers and also plotting to crash a plane loaded with explosives into the US consulate in Karachi, Pakistan.