Last week a court in Brooklyn convicted Al Qaeda operative Adis Medunjanin of plotting to bomb the New York subway.

Bosnian-born US citizen Medunjanin conspired with Najibullah Zazi and Zarein Ahmedzay to launch a major attack before the anniversary of the 9/11 attacks in 2009.

U.S. intelligence and law enforcement officials disrupted the plot before anyone could get hurt, and arrested those involved.

Make no mistake, this plot represented a serious threat to the United States. It was conceived in 2008 by the then head of Al Qaeda’s external operations, Rashid Rauf.

[pullquote text=”Even if an individual is found innocent of all charges before the Military Commissions, the government may decide to keep him locked up.”]Like his two confederates, Medunjanin had attended an Al Qaeda training camp in South Waziristan, Pakistan.

This was a complex case and it showcased all the advantages of using the criminal justice system to prosecute suspected terrorists.

The trial was able to handle sensitive intelligence securely. Several convicted Al Qaeda terrorists, including Zazi and Ahmedzay, actually testified for the prosecution.

Happy to be associated with the trial, the UK government arranged for a former confederate of shoe bomber Richard Reid to address the court from his cell in Britain.

Due process was observed, and the trial was concluded with little fuss and no threat to the general public. To the best of my knowledge there has been no criticism of the verdict either at home or abroad.

It looked like what it was: the exercise of justice.

Now contrast that story with the process that gets under way in Guantanamo tomorrow with the arraignment of Khalid Sheikh Mohammed and his four alleged 9/11 co-conspirators.

It has taken almost a decade for this case to come to court. At Gitmo the rules keep changing. Attorney-client privilege has been violated. Evidence has been withheld. Hearsay is given greater weight than in a criminal trial.

Defense attorneys aren’t even allowed to look at the Wikileaks documents about their clients that are now freely available on the web.

The fact, that some defendants have been tortured has, to date, been treated as a matter of little consequence by the Commissions.

Most troubling of all, even if an individual is found innocent of all charges before the Military Commissions, the government may decide to keep him locked up in the same cell as before as a Prisoner of War for as long as it feels necessary.

If you are acquitted in federal court you leave the building a free man. That is a pretty significant difference.

This is why the majority of defendants before the Military Commissions have ended up striking a plea deal – it is the only way to guarantee that they will eventually get off the island and return home.

No matter how hard the Obama administration tries to repackage the Military Commissions, they are damaged goods.

The optics are horrible, despite the reforms introduced by the Obama administration and the evident professionalism of the military lawyers, there are few people outside the United States who see the Military Commissions as a fair process.

Khalid Sheikh Mohammed and his alleged co-conspirators should have been tried in federal court – like Adis Medunjanin, and the hundreds of other terrorism cases successfully prosecuted in federal courts since the 9/11 attacks.

This was an opportunity to demonstrate to the world the strength of our values and our commitment to fundamental human rights such as the right to due process and a fair trial. It is a test that we have flunked badly.

President Obama had it right on the campaign trial – despite all his tinkering, Military Commissions remain a colossal failure.