Twelve years ago, in Rawalpindi, Pakistan, the man known in intelligence circles as “the mastermind” was dragged bleary-eyed and unkempt from his hideout.

The capture of Khalid Sheikh Mohammed, Al Qaeda’s No. 3, on March 1, 2003, was heralded as an intelligence coup, justice for the Sept. 11, 2001 attacks, a success eclipsed only years later with the killing of Osama bin Laden.

The same, however, cannot be said about Mohammed’s detention and trial.

Twelve years have passed since the 49-year-old was detained; nearly 14 years since the Sept. 11 attacks he is alleged to have orchestrated; seven years since war crime charges were laid against him in Guantanamo.

Prosecuting Mohammed and his four co-accused has proven more difficult than tracking them down in the first place.

Consider what has happened this year alone.

On Wednesday, the military judge presiding over the case, Army Col. James Pohl, froze the pretrial hearings (the trial has not begun and no firm start date is in sight). The Pentagon had ordered him and other Guantanamo judges to move permanently to the remote U.S. base on Cuba’s southeastern shore in an effort to speed the proceedings along.

Pohl stopped the proceedings after defence lawyers argued the Pentagon was trying to unlawfully influence the court. Force Pohl to live in Guantanamo, they reasoned, and he may be more inclined to accelerate the pace of the trial just to get back home.

The hearings and trial could go on for years. Military personnel serving there — usually on six-month rotations — receive $150 extra a month “hardship duty pay.”

The Pentagon rescinded the order on Friday.

“The military commissions have been plagued by intrusions by the FBI, CIA, and now senior DOD officials,” James Connell, a civilian attorney for one of the five men wrote in an emailed statement.

Connell starts his emails with the warning, ATTORNEY COMMUNICATION: DO NOT MONITOR, but lawyers presume everything they send or say is being read and monitored.

That line between paranoia and reality is blurred when it comes to Guantanamo.

A few weeks earlier, the Sept. 11 hearings were again on hold after a defendant recognized a new courtroom interpreter sitting at his defence table. Ramzi Bin al Shibh, a 42-year-old Yemeni captured in Pakistan in 2002, told the judge the interpreter was the same man he had met during his time in a CIA “black site” before his transfer to Guantanamo.

The scenario seemed implausible even for Hollywood — except, a few days later, the Pentagon confirmed that the interpreter had indeed worked for the CIA, although they would not say where.

Then there was the 2013 smoke detector fiasco, when defence lawyers accused some secret agency of listening into their meetings with the Sept. 11 defendants, jeopardizing the sacrosanct right of lawyer/client confidentiality.

No evidence was presented that the meetings were recorded but the Pentagon did release a photo of the devices in the meeting rooms, which looked like smoke detectors but in fact were “Louroe AP-4 audio surveillance units.” Pohl subsequently ordered them removed from the meeting rooms.

Guantanamo’s chief prosecutor, Brig.-Gen. Mark S. Martins, has been the military commissions’ most ardent supporter, but as he conceded in a previous interview with the Star, “this isn’t a game of perfect.”

“The military commissions remain the only forum where we can try people. People can criticize Congress; I can’t. I’m an officer in the army . . . They are elected representatives and they have passed a law that makes it impossible to proceed with any other forum, and we’re going to make this one as fair as it can be,” he said.

U.S. President Barack Obama failed in his effort to bring the men to New York for trial, bowing to the public backlash, and Congress soon after enacted restrictions on prosecuting Guantanamo detainees on U.S. soil.

But Eugene R. Fidell, who teaches courses on military law and Guantanamo at Yale Law School, said he sees no way to salvage the Sept. 11 prosecution in the current system.

“If the test is to inspire public confidence in the administration of justice, that test has failed because by any standard, there have been more misses than hits,” he said in an interview Friday. “Justice has profoundly and inexcusably been delayed. You’ve got a profligate expense to the American taxpayer; you’ve got miscues such as the latest imbroglio over whether the judges were going to have to live at Guantanamo. You’ve got the cases being tossed out . . . It’s a very unimpressive performance for all concerned.”

Of the eight prior Guantanamo convictions, three have been overturned and another three are under appeal in the U.S. courts, including the controversial case against Canadian Omar Khadr. Two of the detainees have had their sentencing postponed.

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“This is really a devil’s brew and a low point in the administration of justice, notwithstanding the claims that have been made of course that this is an established part of our American legal tradition,” said Fidell. “God forbid it should be an established part of our American legal tradition.”

The next pretrial hearing for the Sept. 11 trial is scheduled for April.