A courtroom door opens in Cuba and Khalid Sheikh Mohammed, the self-proclaimed mastermind of the 9/11 attacks, walks in with a uniformed guard holding each shoulder.

As he takes a chair and begins chatting with his lawyers, the man known almost universally as KSM is unrecognisable from the chubby, bleary-eyed fugitive in a white T-shirt shown in the famous photograph of his arrest almost 16 years ago.

His head is shaved and covered by an Afghan wool hat, and he has grown an extensive thick beard dyed orange with henna, which sprawls out over his white robe.

After his 2003 capture in Pakistan he was held and tortured in secret CIA “black sites” in Afghanistan and eastern Europe for three years, before being flown to Guantánamo Bay, the US military zone in south-east Cuba.

The base is now the venue for military tribunal hearings into 9/11 – arguably the biggest criminal case in US history, in terms of its 3,000 murder victims, the breadth of the investigation and its political significance. But nearly seven years after they began, those hearings are only inching forward.

A sketch of the scene inside the courtroom at Camp Justice, as seen through a window. Photograph: Janet Hamlin Illustration/AP

Minutes after Mohammed arrives, his four co-defendants are escorted in one by one: Walid bin Attash, alleged to have run an al-Qaida training camp in Afghanistan where two of the 9/11 hijackers were trained, and Ramzi bin al-Shibh, a Yemeni accused of helping organise logistics for the attack. Both wear camouflage jackets in court, and would have taken part in the attacks, the prosecution says, had they managed to get into the US.

Next is Ammar al-Baluchi, Mohammed’s nephew, alleged to have played a critical role in funding the hijackers and organising their flight school training. The fifth defendant is Mustafa Ahmad al-Hawsawi, a Saudi accused of being a fixer for the 9/11 plot, acquiring cash, credit cards and clothing for the hijackers.

They were first charged in 2008 and the military commission proceedings began in 2012. The accused are growing old, some of the witnesses have died and the trial is still a year off, at least, as the hearings have been bogged down in procedural arguments. The 33rd pre-trial hearing began on Monday.

Separated from the accused by a triple-thick layer of glass, half secluded from observers by a curtain, are a handful of the victims’ families. Cathy Powell’s son Scott was a contractor working in the Pentagon when American Airlines flight 77 hit the building.

For years she tried to flee the constant reminders of her loss.

“I had to move from Washington DC because I couldn’t deal with walking where my son walked,” Powell said. She had expected the law to run its course long ago. And now, 85 and in fragile health, she had come to Guantánamo to try to understand why the case seems to be fading away from the nation’s memory.

Khalid Sheikh Mohammad, who was arrested 16 years ago. Photograph: Janet Hamlin Illustration/AP

“I want justice,” she said. “I think it has gone on too long. Why can’t we get this over?”

The families, the judge, lawyers and approved observers fly in together on a charter plane a couple of days before each hearing, and take a ferry across the bay from the airstrip to Guantánamo’s eastern shore where the courtroom has been established.

Camp Justice is a small outpost enclosed by fences, black netting and coils of razor wire. And it is surrounded by construction equipment, with workers on the go from before dawn to well into the evening. A $14m (£10.5m) upgrade is under way, including a building for defence counsel, and an oversized holding cell for a bedridden inmate.

Barack Obama failed to close the camp, and there are still 40 prisoners left. Only 12 of those have been charged, or soon will be. The rest are stuck in indefinite detention, including five who have been formally cleared but have not been released.

In January 2018, Donald Trump ordered the prison be kept open and predicted that “in many cases” more terrorist suspects could be shipped in. So far, no new prisoners have arrived, but the construction work is a reminder that the military tribunals are likely to remain for some time.

As the defence lawyers, prosecutors and observers lined up to go through security for the first court session this week, they had to negotiate a uniquely local obstacle, a 2ft-long iguana that had taken up position across the court entrance.

The reptiles are protected and the top commandment on the list of ground rules posted around the base is to do them no harm. They seem entirely unfazed by the base’s human visitors.

But for the humans, iguanas are the least of the hazards involved in organising the most complex capital case in the country on a remote island using an improvised hybrid legal system. The events of the past week gave a vivid illustration of some of the reasons the case has dragged on for so long without properly getting off the ground.

On the eve of this week’s hearing, flu ripped through the defence teams, knocking an air force lawyer out of action completely, and afflicting two of the lead counsels, one of them so severely she could barely speak or make her way to the bench.

Defendants shown speaking with their lawyers during a break in proceedings. Photograph: Janet Hamlin/AP

The judge, Col Keith Parrella, insisted on carrying on regardless but with the death penalty at stake, proceedings are not supposed to continue in the absence of any senior defence counsel. With five defence teams including lawyers in their 70s, the chance of the hearings stalling for health reasons are great and increasing.

For all Parrella’s efforts to push on, it was his own medical emergency which brought the hearing to a halt. He was flown out on Wednesday morning for urgent surgery on a detached retina.

Before the judge’s departure, the court had battled over the treatment of a former defence paralegal. Days after leaving Guantánamo, Sgt Brent Skeete had been summoned to Fort Hood army base in Texas on false pretences. He was told he would be briefed on his next deployment, but when he arrived, he was thoroughly searched and interrogated for two and a half hours by FBI agents about the working and personal relationships inside the defence teams. The next day he was polygraphed by officials who just told him they were from “another agency”, a routine euphemism for the CIA.

His account of the incident infuriated the defence, with the lawyers arguing they could not properly represent their clients under the shadow of secret investigations. Parrella consulted with a justice department “special review team” and declared there was no conflict of interest, before hearing the arguments from the defence counsels, only adding to their irritation.

They said Skeete’s experience was just the latest in a litany of acts of harassment and sabotage. Two years ago hidden microphones were found in meeting rooms for attorneys and their clients. David Nevin, Mohammed’s lead attorney, said there was a long history of his former colleagues “being recruited to serve as moles or spies on the defence team”.

“I’m telling you about 10 years of repeated shots across our bow that were false, that were specifically designed to intimidate us and to make us stand back from the fence,” Nevin said. “And it’s gone on long enough. It’s gone on too long.”

James Harrington, Bin al-Shibh’s lawyer, said: “The effect that it had on the members of my team was absolutely devastating. There are still members of my team who were here then who have never fully recovered from that. We had people on our team who wanted to leave right away.”

For the defence, as well as human rights advocates and most legal scholars, the military commissions have been poisoned from their inception by the all-enveloping issue of torture.

The 9/11 defendants arrived in Guantánamo having undergone at least three years of “enhanced interrogation” at CIA black sites. Mohammed was subjected to waterboarding – simulated drowning – 183 times. Hawsawi comes to court with a special cushion and is unable to bear sitting down for long after repeated surgeries made necessary by forced rectal examinations in CIA detention.

The FBI took statements from the defendants in 2007, some months after their arrival in Guantánamo, which included extensive confessions. But the defence lawyers say they were still under the sway of the preceding years of torture, which had left a “learned helplessness”.

Ramzi Bin al-Shibh (centre) is accused of helping organise logistics for the 9/11 attack. Photograph: Janet Hamlin Illustration/AP

For the prosecution, who do not speak to the press, ignoring the 2007 statements would amount to throwing away clear and decisive evidence. An appeal filed last year said: “The statements made by the accused to the FBI constitute acknowledgments of guilt and responsibility for the largest act of terrorism in the history of the United States.”

The status of the 2007 testimony in an eventual trial has yet to be finally decided. For now, the prosecution is disqualified from using the 2007 statements and the defence is blocked from trying to locate or contact any CIA officials or contractors, current or former, who were involved in the rendition programme, or their friends, family or colleagues.

In order to contact anyone involved in the programme, the defence has to go through the government.

For the defence lawyer Alka Pradhan, the obstacles to investigating what happened in the black sites are just the latest effort to cover up state-sponsored torture, which, for her, is in the dock alongside the accused.

“There has always been a deliberate effort by the government to keep these proceedings secret and my opinion is that if the public actually saw what was going on down here, they would be outraged,” Pradhan said.

“There has never been any reckoning in the United States regarding the torture programme.”

There are several other constraints on the defence that would be unthinkable in federal court, especially in a death penalty case. It is not allowed to reveal classified information, but in a touch of Kafka in the Caribbean, the government has not provided clear guidance on what is classified and what is not. Even more importantly, the defence cannot call its own witnesses but must go through the government, which attorneys claim has turned down 90% of its requests.

“This is by definition a broken system. If the purpose of all this is justice, no one is getting any,” said Brig Gen John Baker, who oversees all the defence teams at Guantánamo. “The bedrock principle of our nation is justice, due process and rule of law, making sure people get proper representation. Our system is on trial here. The defence are the only ones standing up for the system.”

After witnessing the procedural cut and thrust, with little apparent forward movement, Powell declared herself as bewildered as when she first arrived in Guantánamo over the weekend, looking for answers about her son’s death.

“They are just saying the same thing over and over and over again,” she said.

Had coming to the camp and seeing proceedings firsthand brought any peace? “No,” she said. “When it’s over, it will.”

• This article was amended on 8 February 2019. An earlier version described Guantánamo as a “US military enclave”; this has been changed to “US military zone”.