A Guide to the Bali Bombing Case of Three Prisoners at Guantánamo Bay

Three prisoners at Guantánamo Bay are accused of terrorism, murder and conspiracy in bombings in Indonesia 20 years ago as members of Jemaah Islamiyah, an extremist group founded in the 1980s with the goal of establishing an Islamic state in Southeast Asia.

In one attack, a suicide bomber and a truck bomb detonated at nightclubs in Bali in October 2002, killing more than 200 people, mostly Australians and Indonesians as well as seven Americans. Then, in August 2003, 11 people were killed in a car bombing at a Marriott hotel in Jakarta.

The U.S. government considered both attacks acts of war that were carried out by an affiliate of Al Qaeda after the attacks of Sept. 11, 2001, making them eligible for trial by a military commission at Guantánamo Bay.

The charges, which also include attempted murder, carry a maximum punishment of life in prison.

All three men were held by the C.I.A. in the early years of their detention and were tortured, according to their defense lawyers.

Prosecutors have proposed to hold the trial in 2025.

The defendants were arraigned in August 2021, 18 years after they were captured. Prosecutors had been pursuing the case since at least 2016, when the chief prosecutor at the time, Brig. Gen. Mark S. Martins, traveled to Malaysia with a State Department official to discuss a proposal for one of the defendants to serve his sentence there, in exchange for a cooperation agreement. A deal was never reached.

Prosecutors continued to work on the case, and a Trump administration appointee made the decision to charge the men on the second day of the Biden administration. Their arraignment was delayed by the coronavirus pandemic.

A total of 213 people were killed in the attacks, according to the charges. In addition, an appendix to the charge sheets names 31 survivors, three of them Americans who were injured in the Marriott bombing.

Prosecutors sponsored a visit to a hearing in April 2023 by relatives of four British victims who had traveled to Bali, a popular island vacation spot, for a rugby tournament.

Survivors or their family members can go to Guantánamo as guests of the prosecution to observe a week of hearings. Their travel, hotel and chaperones are provided through the Pentagon’s Victim/Witness Assistance Program, which receives funding from the Justice Department.

Lt. Col. Wesley A. Braun of the Air Force, who is based in Texas, was assigned to the case on July 28, the same month he began his second stint as a military judge. He was previously on the bench for 32 months from 2018 to 2021 and based in Virginia. This is his first military commissions case. He was commissioned in the Air Force in 2006, the year he graduated from Michigan State University College of Law.

Capt. Hayes C. Larsen of the Navy presided at the first two hearings, starting with the arraignment in August 2021, then left the case in July. Captain Larsen had repeatedly ruled, despite protests from lawyers that the defendants could not understand some of the proceedings, that foreign language translation of the proceedings provided by the U.S. government has been adequate.

U.S. intelligence reports say he rose to the role of “operational mastermind” of Jemaah Islamiyah and in the late 1990s dispatched followers, including his two co-defendants, to Afghanistan to train on terrorist techniques. He was captured in a joint U.S. and Thai intelligence raid outside Bangkok in August 2003 and held incommunicado in a secret C.I.A. prison network for the next three years.

A Senate study found that he was subjected to treatment that was so heinous that a U.S. interrogator told Mr. Hambali he “would never go to court because ‘we can never let the world know what I have done to you.’”

The study also discredits the agency’s claims that intelligence extracted from him provided new information in the war against terrorism. It questioned whether Mr. Hambali, taking his cues from his interrogation, told C.I.A. employees what they wanted to hear. He later recanted, according to the Senate study, and C.I.A. officials found those retractions credible.

He was transferred to Guantánamo Bay in September 2006, ostensibly for trial, but he was not formally charged until his first court appearance in August 2021.

A native of Malaysia, Mr. Bin Lep has been described by U.S. intelligence as a “key lieutenant” of Mr. Hambali. U.S. officials say his alias, or nom de guerre, is Lillie. He is accused of traveling with his co-defendant Mohammed Farik Bin Amin to Afghanistan in 2000 for jihadist training. Prosecutors say that during that time, Mr. Bin Lep guarded Taliban positions in battles with Northern Alliance forces.

His criminal charges say that after the Sept. 11 attacks, he and Mr. Bin Amin traveled throughout Southeast Asia and conducted surveillance of potential targets for terrorist attacks, including an Israeli airline counter at the Bangkok airport. He is also accused of smuggling weapons in Thailand as part of plotting for post-9/11 attacks. He was captured on the same day as Mr. Hambali outside Bangkok in August 2003 and spent the next three years in C.I.A. prisons.

Mr. Bin Amin, also a native Malaysian, was captured two months before his co-defendants in Thailand and turned over to the C.I.A., which held him incommunicado until he was transferred to Guantánamo Bay in 2006. U.S. officials say his alias, or nom de guerre, is Zubair. U.S. intelligence has also called him a “key lieutenant” of Mr. Hambali who trained in Afghanistan, scouted potential targets with Mr. Bin Lep and was a go-between who received about $50,000 in Bangkok that was eventually used to fund the Marriott bombing.

The charges say that Mr. Bin Amin and Mr. Bin Lep spent several months before the Sept. 11 attacks at a guesthouse in Afghanistan that was run by Mr. Hambali and that both men met with Osama bin Laden and agreed to take part in unrealized suicide operations aimed at American targets.

The lead prosecutor in the case is Col. George C. Kraehe of the Army, a lawyer from the national security division of the Justice Department who was mobilized to serve as a war court prosecutor. Other team members include Maj. Imelda U. Antonio of the Air Force; Lt. Col. Joshua S. Bearden and Capt. Marcus J. Colicelli of the Army; and Lt. Patrick R. Rigney and Lt. Jeffrey M. Larson of the Navy.

The chief defense counsel is Brig. Gen. Jackie L. Thompson Jr. of the Army.

Mr. Hambali is represented by James R. Hodes, a civilian who serves as lead counsel with Cmdr. Eric S. Nelson and Lt. Ryan Hirschler of the Navy; Lt. Col. Geoffrey S. DeWeese of the Army; Maj. Cristina D. Curl of the Air Force; and David Akerson, a civilian.

Mr. Bin Lep is represented by Brian Bouffard, a civilian who serves as lead counsel and previously served in the Navy as a lawyer, with Maj. Jason Cordova of the Air Force; Lt. Jennifer Joseph of the Navy; and Aaron Shepard, a civilian.

Mr. Bin Amin is represented by Christine A. Funk, a civilian who serves as lead counsel; Lt. Col. Chantell Higgins of the Marines; and Lt. Cmdr. Crystal Curtis of the Navy.

In 2021, the Pentagon began building another courtroom at Guantánamo Bay with capacity to put three defendants in a single case on trial. Up to six prisoners can be tried in the main courtroom, and the goal was to hold two hearings simultaneously. But the new $4 million chamber was still not ready in the summer of 2023, and judges rescheduled cases to avoid schedule conflicts.

Part of the delay in opening the court was caused by a court decision to add a special gallery for the public to watch the case live, but listen on a 40-second delay — a feature that was configured in the larger courtroom but that was initially left out of the smaller court.