Ahmed Omar Abu Ali, the American citizen accused of plotting with Al Qaeda to assassinate President Bush, will have his guilt judged in an American court. What we can say now is that his case seems to be another demonstration of what has gone wrong in the federal war on terror.

Mr. Abu Ali, 23, was arrested by Saudi officials in a crackdown after terrorist bombings in Riyadh in 2003. But the Saudis have never shown much interest in actually charging him with a crime. His parents claimed that he was being held at the behest of the United States, and sued in court to get him returned to this country. A federal judge has said that "there has been at least some circumstantial evidence that Abu Ali has been tortured during interrogations with the knowledge of the United States."

The Justice Department says Mr. Abu Ali, who went to Saudi Arabia to continue his religious studies, got Al Qaeda training and money from terrorist associates to buy a laptop computer and books. The indictment also says Mr. Abu Ali talked about assassinating Mr. Bush either by getting "close enough to the president to shoot him on the street" or figuring out a way to kill him with a car bomb.

If the Justice Department believed that Mr. Abu Ali was a serious terrorist, he should have been brought back here long ago for trial. Instead, he became part of an unknown number of prisoners who were swept up by American officials or foreign governments working with Americans and questioned in the wake of Sept. 11. Many were then held indefinitely and, in some cases, tortured in hopes that they would provide information.

The civil liberties issues have always been evident, but now the practical consequences are becoming clearer as well.

In an undisciplined attempt to wring statements out of any conceivable suspect, American officials have worked with countries like Saudi Arabia, a nation whose attitude toward human rights is deplorable, and Syria, which is counted by Washington as a state sponsor of terrorism. And now these officials are faced with the problem of what to do with these prisoners, most of whom have proved to be no use to interrogators, but who remain on America's conscience.