The trial of the alleged masterminds of 9/11, which began last week at the U.S. Naval Base in Guantanamo Bay, Cuba, will address some of the most profound issues of our era. Are natural rights truly inalienable, as Thomas Jefferson wrote in the Declaration of Independence, or can the government take them away from those it hates or fears? Does the Constitution protect the rights of all persons who come in contact with the government, or does it protect only certain Americans, as the government argues? Can the government deny a person due process by changing the rules retroactively, or is the Constitution's guarantee of due process to all persons truly a guarantee?

These are all questions that the government does not want to answer. But it should know better, because by structuring the trial after the crime was committed and by establishing retroactive rules—which are prohibited by the Constitution—that have never before been used in any American civilian or military court, Congress has created and the Obama administration will conduct a trial that will resemble none in our history.

The trial is being held in Cuba because President Obama caved to political pressure from New York City politicians who did not want the trial at the location where the murders took place. In one of the few rules of criminal procedure laid down in the Constitution itself, the Framers required all trials to be held in the same judicial district where the alleged crime took place. They were familiar with the British practice of trying colonists in London for alleged crimes committed in New York. But today New York politicians and their allies in Congress and the president think they can pick and choose which parts of the Constitution to uphold and which parts they can ignore.

The Constitution guarantees the right to confront evidence and witnesses. The colonists were all too familiar with Star Chamber, a British trial system in which evidence against an accused was summarized by a clerk of the court, rather than presented by witnesses with personal knowledge or revealed in documents for all to see. In trials at Gitmo, the government may summarize evidence for the court, and it may keep documents it plans to use away from the defendants.

The rules for this trial also permit hearsay: basically, anonymous accusations that were also the hallmark of Star Chamber. They permit the Secretary of Defense, who is the boss of both the prosecutors and the judge, to replace the judge if the secretary is displeased by his rulings. This is a procedure that is taken right out of the Communist Party playbook in Stalinist Russia.

Perhaps the most radical departure from American due process and pronounced return to Star Chamber is the congressional authorization for the admission of evidence obtained under torture. There is no question that these defendants were tortured. The CIA has admitted publicly that it waterboarded one of them 183 times and then destroyed the videotapes of the torture so jurors could not see how horrific this procedure is.

Torture is so abhorrent to American values that its use by rogue cops has resulted in what is known as the "shocks the conscience of the court" rule. This principle, which has been in place since colonial times, permits the court to dismiss the charges—no matter how grave—when the government's behavior shocks the conscience of the court. And all intentional torture is in that category.

I understand the emotions that are fueling these prosecutions, and I understand the pain and loss suffered by those whose loved ones were murdered on 9/11, and I understand the horrific nature of the crimes for which these defendants have been charged. But in America, we still have the rule of law. And that means that no one is above the law and no one is beneath it. Everyone is subject to the law, and the government may not exclude anyone from its protections. That is the essence of our system of justice. It is mandated by the Declaration of Independence and the Constitution, and its preservation is the reason we have fought our just wars.

This trial may have dire unforeseen consequences. From the president who opposed all this when he was a senator but now effectuates it, to members of Congress who enacted the Military Commissions Act that authorizes incarceration after acquittal (a procedure even the Soviets did not utilize), to the victims' families who surely would not want this rough justice visited upon their children; all these people now crying for blood could one day see the ruination of due process in America, with this case as precedent.

What constitutes a fair trial is the due process of American justice, which is guaranteed and required by the Constitution itself. If we deviate from the moral values of that system for the people we hate, woe to us for making law retroactively and based on hatred.

Andrew P. Napolitano, a former judge of the Superior Court of New Jersey, is the senior judicial analyst at Fox News Channel. Judge Napolitano has written six books on the U.S. Constitution. The most recent is "It Is Dangerous To Be Right When the Government Is Wrong: The Case for Personal Freedom."