Of the seven cases decided by military commission, five were guilty pleas, and the two that went to trial were overturned on appeal. Because of those two appellate losses for the government, prosecutors at Guantánamo can’t charge defendants with conspiracy and material support of terrorism before 2006 — the very charges Abu Ghaith is facing in federal court. Whether Guantánamo prosecutors can bring conspiracy charges for acts committed after 2006 remains an open question.

A comparison of the two processes is stark. Terrorism cases at Guantánamo — called military commissions — operate in a legal framework that is a combination of civilian and military law with virtually no case history or legal precedents. No trial date has been set for Khalid Sheik Mohammed and his four co-defendants in the so-called 9/11 trial, nor is a date likely in the near future. The commission for Abd al-Rahim al-Nashiri, an alleged plotter of the USS Cole bombing, is set for December, but even if that trial opens on time, it could still drag on for years in a complicated appeal process.

The Abu Ghaith trial, however, has ramifications beyond the the case itself. Holding such a high-profile terrorism trial in a criminal court in New York has cast a fresh spotlight on the stark differences between it and the hearings being held in Guantánamo Bay, which have been condemned by civil liberties groups in the United States and abroad. That is especially true because one of the main justifications for those hearings — and of the controversial Guantánamo detention center — is that terrorism trials are too difficult to hold in a normal court.

Yet the high-profile terrorism case, in which the defendant unexpectedly took the stand, was defined by clarity and speed of process. “It was a by-the-books trial, even with him testifying,” said Karen Greenberg, author of “The Least Worst Place: Guantánamo’s First 100 Days.” “And that’s a good thing.” Both sides offered closing arguments on Monday, after which the jury began its deliberations.

This scene, which took place shortly after opening arguments in the trial of Sulaiman Abu Ghaith — Osama bin Laden’s son-in-law and an alleged spokesman for Al-Qaeda — was not the only time the judge reprimanded Cohen for pushing boundaries.

In a dark wood-paneled federal courtroom in lower Manhattan, defense attorney Stanley Cohen recently pressed FBI special agent James Fitzpatrick about his more than a decade of experience investigating Al-Qaeda. The vigorous cross-examination drew repeated objections from the prosecution, nearly all of which were sustained by Judge Lewis Kaplan.

Beyond the confusion on the scope of available charges, defense attorneys at Guantánamo regularly complain about a lack of clarity in the rules that govern the proceedings. One example is Guantánamo’s rule that governs hearsay, which is generally prohibited in federal court. In the Guantánamo military commissions, however, the aperture for admitting hearsay is significantly greater — as is the case in military courts martial.

As a result, attorneys at Guantánamo fear that their clients may find themselves in positions where they can’t face their accusers. “The hearsay rules are detailed and well-established in federal court and backed up by the Sixth Amendment confrontation clause,” said James Connell, a civilian attorney for Amar al-Baluchi, a defendant in the 9/11 trial.

The commission rules allow hearsay after a test is conducted on the evidence to see if producing a witness would hurt military or intelligence operations. That could mean statements from other alleged Al-Qaeda members, military contractors or FBI and CIA agents and operatives could be used at commissions to incriminate defendants even if those parties never appear court.

But how that rule will actually play out in court remains unclear, in part because the applicability of the Sixth Amendment — which governs the production of witnesses in court as part of the Bill of Rights — has so far been unanswered at Guantánamo. “The judge has ruled that we will have to take up the applicability of the Constitution, including the Sixth Amendment, on a case-by-case basis,” said Connell in an email to Al Jazeera America. “No one knows what that rule of evidence means or whether it is constitutional or whether the Constitution even applies.”

But the commissions’ chief prosecutor, Brig. Gen. Mark Martins, has taken umbrage at the idea that the Constitution doesn’t apply at Guantánamo. He and other defenders of the process have pointed out that the Constitution is more than the Bill of Rights, that Congress passed the Military Commissions Act of 2009 after a previous version was invalidated by the Supreme Court and that all three branches of government have weighed in positively on the legality of the commissions.

Yet legal questions aside, there remain significant and obvious differences between the two systems. For one, there is scarcely an easier place in the United States to get to than lower Manhattan. Court is open to the public and the press with few restrictions, and when Abu Ghaith took the stand, a second room was made available for the spillover because of high media interest. Guantánamo, by contrast, is accessible only to a small number of people, including victims of 9/11 and the 2000 bombing of the USS Cole, as well as reporters and human rights workers, who must agree to restrictive guidelines to attend.

Rita Lasar, whose brother was killed in the north tower of the World Trade Center on 9/11, has attended proceedings for Abu Ghaith and at Guantánamo and thinks the 9/11 trial should take place in civilian court. The courtroom in New York “was so ordinary, I was struck by the difference,” she said in an email. “The jury was made up of ordinary New Yorkers, those people most affected by the events of 9/11.” In the commission system at Guantánamo, the jury — known as a panel — is composed of military officers.

Lasar also noted that in federal court there is no physical barrier between the public and the trial, unlike at Guantánamo, where three panes of soundproof glass separate media, family members and NGO representatives from the enormous commission room.

Instead of hearing what’s happening not more than a few feet away, observers must wait 40 seconds for a delayed feed to appear on overhead monitors. If the Guantánamo court security officer thinks someone has disclosed classified information, he hits a button that cuts the feed and triggers a red, spinning light like a hockey game’s. In one instance, a third party — apparently acting as a censor and unknown to the judge — cut the feed, creating pandemonium and confusion in the court, not to mention undermining the judge’s authority.