The Road We Need Not Have Traveled The Pentagon's prosecutors formally charged Khalid Shaikh Mohammed and four other men last week with war crimes for planning and carrying out the murder of 2,976 people on Sept. 11, 2001, and referred their case to a constitutionally flawed military tribunal that will be convened at the Guantánamo Bay detention camp, a global symbol of human rights abuses. The conspirators have been held for more than nine years. As Brig. Gen. Mark Martins, the chief military prosecutor, said in a speech at Harvard on Tuesday, the use of military commissions "has become a matter of the rule of law and of recognizing that at some point justice delayed really is justice denied." But it is worth remembering how we got to this system and this place - the worst way to administer justice to the 9/11 terrorists. Let's start with the delay. All of the men could have been brought to trial years ago, but President Bush decided he could ignore the Constitution. He ordered them to be held in secret C.I.A. prisons and subjected to brutal and illegal interrogations. Mr. Mohammed was waterboarded 183 times in one month alone. That torture produced no useful intelligence, according to virtually all accounts, except those offered by people like former Vice President Dick Cheney, who was the key architect of the Bush administration's lawless detention and interrogation policies. When Mr. Mohammed was moved to Guantánamo Bay, finally, with the four others, there were immediate questions about whether they could ever be tried legitimately, given how tainted the evidence was. Mr. Bush did nothing, content with arguing that Congress's decision to declare a perpetual state of war with Al Qaeda gave him the right to hold prisoners indefinitely without any trial. President Obama came into office pledging to close Guantánamo Bay and restore the rule of law to the treatment of terrorism suspects. He has largely failed. Attorney General Eric Holder Jr. announced that the Justice Department had reviewed the cases against these five prisoners and concluded they should be tried in federal court in Manhattan. He was absolutely right, but he failed to prepare local politicians, who claimed the trial would pose a security threat - a problem, if it ever existed, that could have been dealt with. The posturing on Capitol Hill was worse, with Republicans howling that a civil trial would not guarantee a guilty verdict, the law be damned. The White House put the trial on hold, and Congress meanwhile passed a law prohibiting the use of federal money to try any Guantánamo prisoner in federal court. The Justice Department then "reviewed" the cases again and announced that what it really meant was these were prisoners who were best handled by a military tribunal. And so there will be a trial - in a tribunal system improved from the kangaroo courts that Mr. Bush created, but still profoundly flawed. At Harvard, General Martins spoke eloquently about the need for real justice. "If we treat the law as a luxury, we sacrifice legitimacy," he said. Those are powerful words, but can he keep that promise? Jameel Jaffer, deputy legal director of the American Civil Liberties Union, notes that after years of being subjected to treatment designed to destroy prisoners physically and psychologically, "if someone emerges from this kind of system and then supplies a confession or a guilty plea, how confident can we be that the statement is untainted by torture? Imagine that another country - Iran, say, or North Korea - proposed as much. Would we buy it? We hope General Martins's commitment to justice will persuade a highly skeptical world to accept the legitimacy of these trials; convicting and executing the prisoners after a tainted trial would be a disaster. But after all that has happened, even the best-managed trial will not be able to change the fact that this country has in the last decade accepted too many damaging and unnecessary changes to its fundamental principles of justice and human rights.