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An unavoidable consequence of creating a new and ad hoc justice system on the fly is that issues that would be simple and routine in an ordinary criminal trial end up raising questions that are novel and highly contested. This has been a regular feature of the Guantánamo military commissions. We travel here to observe "pre-trial proceedings" with the expectation that the cases will be moving towards trial — only to find out that, because of some arcane dispute about what the new rules mean, trial has become even more remote.

Day Two of the proceedings in the case of Ibrahim Ahmed Mahmoud al-Qosi provided a case in point. Lt. Col. Nancy Paul became the first military commissions judge to apply the Military Commissions Act of 2009 (MCA of 2009) to one of six cases that were pending at the time the act was passed. Both sides won something and lost something in her decision on the government's motion to amend the charge sheet.

The judge read from the bench (PDF) on the government's last-minute motion to amend the charge sheet, which accuses al-Qosi of conspiring with Osama bin Laden and al Qaeda and providing material support for terrorism. Confronted with an effort by the government to capitalize on the recent passage of the MCA of 2009 to dramatically expand the charges against al-Qosi, she pushed back.

As I explained in my previous post, the MCA of 2009 changed the jurisdiction of the military commissions from presiding over the trials of "unlawful enemy combatants" to those of "unprivileged enemy belligerents" — individuals who lack prisoner of war (POW) status as defined by the Third Geneva Convention. The government moved to amend the charges against al-Qosi to bring them in line with the new jurisdictional basis of the military commissions.

But the government's proposed amendments went far beyond what the MCA of 2009 requires or even permits. They sought to replace the nine overt acts that al-Qosi is alleged to have conducted as a part of a conspiracy to commit war crimes with 12 new overt acts, and to expand by four years the time frame in which al-Qosi allegedly engaged in conspiracy and material support for terrorism. The amended charge sheet would allege that al-Qosi started engaging in illegal conduct back in 1992 (rather than 1996) and that he did so in, among other places, Ethiopia, Somalia, and Chechnya.

Al-Qosi was firstcharged in 2004. The charges against him were amended in 2008. His defense counsel have spent years preparing his defense in response to the latest set of charges. Adding new charges at this late date potentially would require the defense to reinvestigate the entire case in foreign lands.

Lt. Col. Paul saw through the government's argument that these vast changes were needed to conform the charges to the MCA of 2009. Reasoning from the old rules promulgated to apply to the Military Commissions Act of 2006 and from the Uniform Code of Military Justice rules governing the amendment of charges, the military judge granted the government's motion to replace the phrase "unlawful enemy combatant" with the new "unprivileged enemy belligerent." But she denied the remainder of the motion as an effort by the government to "fundamentally" change the charges against Al-Qosi, holding that the requested amendments "dramatically change[...]the nature of the facts alleged" and brought "unfair surprise" to the accused.

The military judge got it right this time. Permitting the government to expand both the time frame and substance of the allegations against al-Qosi after he has already spent two years defending himself against the 2008 charges would be fundamentally unfair.

But the ruling does little to ensure that al-Qosi will get a fair trial in the military commissions, because the government can now simply withdraw the charges against al-Qosi and return to the Convening Authority to seek a charge sheet that includes all of the additional facts it wants to plead. Should the government do so, where will that leave al-Qosi? After nearly eight years of detention in Guantanamo Bay, al-Qosi will be even further away from a trial. He will be arraigned and will go through the process of choosing counsel again. And the public will have spent millions of dollars supporting military commissions that have yet to provide a fair trial — and are structurally incapable of doing so.

As the judge read her rulings on Thursday, I thought of how the novel legal issues she reached would have been avoided had Attorney General Holder chosen to prosecute al-Qosi in federal court. Both of the crimes with which al-Qosi is charged — conspiring with Osama bin Laden and al Qaeda and providing material support for terrorism — could be prosecuted in federal court. Neither is a war crime traditionally prosecuted in a military commission. And in federal court, we would not spend many years and untold resources squabbling over preliminary issues of fundamental fairness to the accused.

These issues are still not resolved in al-Qosi's case. The judge has yet to rule on three defense motions to dismiss the case, two of which highlight that the military commissions are inherently illegitimate — a separate and vastly unequal system created from scratch to prosecute non-citizens whom the federal government believes it may not be able to convict in federal court. This system violates the Constitution and international law and undermines our commitment to the rule of law.

The government should indeed withdraw the charges against al-Qosi. But if it seeks to try him on a new set of charges, it should do so in a federal court that will provide due process and other much needed fair trial protections.