Two Malaysian men who have been in US custody for two decades have been sentenced by a military jury to 23 years in confinement, for conspiracy in connection to the 2002 Bali bombings.

However, due to a pre-trial agreement that remained secret until the end of the proceedings, both men will only serve about five years of their sentences.

Mohammed Nazir Bin Lep and Mohammed Farik Bin Amin struck plea deals with prosecutors last year, 20 years after their arrests in Thailand in 2003.

They have been held at Guantanamo Bay since 2006, but were not charged until 2021.

They were initially charged alongside the man accused of being their ringleader, Hambali, an alleged leader of the Al-Qaeda-linked terror group Jemaah Islamiah.

Prosecutors originally alleged Hambali was the “operational mastermind” of the attacks, and that Bin Amin and Bin Lep were “key lieutenants” who provided support, including acting as money couriers, after travelling to Afghanistan for jihadist training.

Evidence given by the men is likely to be used when Hambali goes on trial in Guantanamo Bay in March next year.

Several days of sentencing proceedings were this week held at Guantanamo Bay and livestreamed to several other US military bases.

It took a panel of jurors, assembled from the armed forces, a little over two hours to deliberate.

Time already spent in custody will not count towards the men’s sentences.

The bomb attacks on the Sari nightclub and Paddy’s pub in Kuta killed 202 people, including 88 Australians.

Three Bali bombers were executed by firing squad in Indonesia in 2008, five years after they were sentenced.

Prosecutor implores jury to ignore pleas for mercy

During the hearing, which lasted less than three days, lead prosecutor Colonel George C Kraehe harked back to the 1990s, when Al Qaeda leader Osama Bin Laden declared war on America and Western civilisation.

“The accused heeded Osama bin Laden’s call,” he said.

“In 2000, they travelled to Afghanistan where they received instruction in jihad. They knowingly and voluntarily took part in Al Qaeda’s war.”

Colonel Kraehe said the men were trained in basic military tactics and Bin Laden himself lectured them about the need for violent jihad.

Earlier, both men gave statements to the court renouncing violence in the name of Islam. They spoke of loving families who hadn’t raised them to hate the West, and asked for mercy.

“The accused want your mercy,” Colonel Kraehe told the jury.

“But in considering the accused’s request for mercy, ask yourselves: where was their mercy for the victims? There was none.

“They should be shown exactly the same mercy they showed the dead, the injured, and those left behind: none at all.” 

Defendants apologise, claim they were tortured

During the proceedings, Bin Amin admitted travelling to Afghanistan to participate in military training.

“I didn’t know anything about the Bali bomb until after it happened,” he said.

He went on to say he did agree to transfer money afterwards, which he knew would be used to help people who had been involved, but said he did not know any details.

He said he was deeply sorry to the victims, and that there were no words to express his remorse.

The court was shown pictures he’d drawn of his alleged treatment in US custody. They depicted him being stripped naked and shackled to walls, the ceiling or the floor. One drawing showed a man pouring cold water over him as other men held him down.

“I am uncomfortable talking to you about my torture. I’m not trying to compete with the victims’ pain,” he told the court.

Bin Lep also gave a short statement. He too apologised for his actions and said they were not what was taught to him by his family or community.

“I know that the victims and their families deserve more than words but I still want to say I am sorry,” he said.

“I received pictures of some of the victims and I will carry the faces in my mind for the rest of my life.

“My actions were wrong and I will live with what I did forever. This is why I have cooperated … and will continue to do whatever is asked of me.”

Bin Lep said he was also tortured in US custody.

“I have seen Mr Bin Amin’s drawings and most of those acts were done to me,” he said.

“There were things done to me that were not in his drawings … but I do not wish to talk about it.”

Guantanamo Bay, the US’s military prison in Cuba, held about 600 detainees at its peak. About 30 detainees remain there.

‘An incalculable, stupid, terrible waste’

People from 22 countries were killed in the bombings. 

Family members who lost loved ones in the terror attack travelled to Guantanamo Bay to give victim impact statements to the court in person. 

For several hours, the panel of jurors was shown photographs of young people who were killed, all pictured looking happy and vibrant. 

Bin Amin and Bin Lep were also in the courtroom as parents and siblings described their loss. 

The parents of two young American women, Deborah Lea Snodgrass, 33, and Megan Heffernan, 28, who were both teaching English overseas, described the pain of losing their kind, adventurous daughters.

“Megan was truly a personification of joy and love,” said her father, Frank Heffernan. He went on to say that her mother had preserved all her things, and her siblings had tattoos of her face.

“Our family is not complete without Megan … those involved in the bombing robbed us of the many years we could have seen her smile, pulled her close, heard her voice on the end of the phone.”

His wife, Megan’s stepmother Bonnie Hall, also gave a statement.

“It’s an incalculable, stupid, terrible waste. One of many I’m afraid. One of 202,” she said.

Christopher Snodgrass, Deborah’s father, said his daughter had been an amazing person – inclusive, kind, a lover of animals and a “positive light” for all who knew her.

He said the circumstances of her murder had darkened his view of Muslims.

“I’m a religious person, and the hate-filled person I’ve become is certainly not what I wanted,” he told the court.

The sisters of Dimitris Panagoulas, 28, spoke of a kind, brave and community-oriented young man who was running a business with his father and had gone to Bali to surf.

Mr Panagoulas, who was Greek, was airlifted to Darwin with burns to more than 80 per cent of his body. He died in hospital two days after the bombings.

His family didn’t know where he was for a month.

His youngest sister Eleni described how an older sister had travelled to Bali and looked through charred bodies for their brother.

“They say time heals all, but that is simply a lie,” she said.

Maggie Stephens, from Worcestershire in the UK, lost her 27-year-old son Neil Bowler, who’d been living in Singapore and had travelled to Bali for a rugby tournament.

“It was Liz, his partner, who had remained in Singapore who had to ring me on that fateful day … what a thing to have to do,” she said.

The court heard the couple had been together since university, and that his mother drew great comfort from the knowledge that he’d found his soulmate.