Nearly six years ago, President George W. Bush declared Ali Saleh Kahlah al-Marri an enemy combatant and had him swept out of federal court and into a U.S. Navy brig so he could be interrogated without the legal protections afforded by the criminal justice system. Bush said the Qatari national, arrested as a material witness in Illinois in December 2001, possessed critical intelligence that "would aid U.S. efforts to prevent attacks by al-Qaeda on the United States."

In an agreement Marri entered Thursday in Peoria, Ill., he pleaded guilty to conspiracy to provide material support to al-Qaeda and admitted to being a sleeper agent. Under the guise of being a student, Marri came to the United States on Sept. 10, 2001, on the orders of Khalid Sheik Mohammed, the self-proclaimed mastermind of the Sept. 11 attacks, and began to research the use of chemical weapons as well as potential targets, according to the plea.

Thursday's agreement calls for a maximum sentence of 15 years -- a penalty that could be reduced by several years if Marri gets credit for time already served. By removing Marri from the courts in June 2003, the Bush administration effectively sacrificed the ability of prosecutors to throw the book at Marri when he was returned to the system, military and legal experts say. And the Marri case suggests that as the government pushes forward with plans to prosecute detainees held at Guantanamo Bay, Cuba, it may again have to accept lesser sentences for those who were subjected to physical and psychological abuse.

There are up to 100 detainees in Guantanamo who are too dangerous to release but who cannot be tried, according to Pentagon estimates. In many cases, such as Marri's, their prosecution in federal court carries risks that the government will have to make public classified material or endure new revelations about abuse during detention and interrogation.

The fear that some Guantanamo cases are not prosecutable in federal court has sharpened debate within the Obama administration about the need to maintain military commissions, in which the rules of evidence are less stringent, according to sources involved in the discussions. Obama criticized such tribunals during the campaign, but some of his top officials, including Defense Secretary Robert M. Gates, have said in recent days that the commissions remain an option.

Responding to complaints from military groups that Marri's sentence is too short, a Justice Department spokesman said the possible 15-year term was the best deal the government could strike, given concerns about the release of classified evidence and the impact of possible testimony regarding Marri's mental state after prolonged solitary confinement.

Marri "is a good example of how the government is going to have to accept some compromise outcomes in tough cases, and we will see this kind of outcome over and over again as they go through the Guantanamo cases," said Matthew Waxman, a Columbia University law professor and a former Pentagon official in charge of detainee issues during the Bush administration. "The history and controversy of this case boxed in the current administration and they were probably loath to litigate it, in part not to have to defend past practices but also because of litigation risks, including acquittal."

Since Marri and potential witnesses in his case, including Mohammed, were interrogated using techniques later suspended by Obama, it is possible the court could toss out statements obtained under duress. Defense lawyers said in court papers that interrogators threatened Marri, telling him he would be transferred to Saudi Arabia or Egypt, where he would be sodomized and forced to watch the rape of his wife.

For the defense, the plea also had benefits. Marri, 43, eluded a 30-year prison sentence if an American jury, unlikely to be sympathetic to a cohort of Mohammed's, had found him guilty of material support rather than the conspiracy charge to which he pleaded guilty. In the plea agreement, the government dropped the material-support charge.

Marri came to the United States to study and graduated from Peoria's Bradley University in 1991. He later attended al-Qaeda training camps in Afghanistan and was approached by Mohammed, who appreciated his command of English and his having lived in the United States. The two created codes for e-mail and phone communication once Marri reached the United States, according to the plea agreement.

On the way to Illinois, where he had reenrolled at Bradley, Marri stopped in Dubai to pick up $10,000 from Mustafa al-Hawsawi, who allegedly financed the Sept. 11 hijackers. Hawsawi is now being held at Guantanamo Bay.

Marri's sentencing is set for July 30. He still has the opportunity to argue that he should be credited for the time spent in the brig.

During plea negotiations, Attorney General Eric H. Holder Jr., who took a personal interest in the case, firmly opposed giving Marri any credit for his time served in military custody, according to Justice Department officials.

"Without a doubt, this case is a grim reminder of the seriousness of the threat we, as a nation, still face," Holder said in a statement. "But it also reflects what we can achieve when we have faith in our criminal justice system and are unwavering in our commitment to the values upon which this nation was founded and the rule of law."

Lawyers for Marri say justice demands that their client get a sentence of no more than 10 years.

"I think it would be an outrage if he was given no credit for the period when he was stripped of his rights," said Jonathan Hafetz, a lawyer with the American Civil Liberties Union's National Security Project, who represented Marri in habeas proceedings while he was in the brig. "The torture culture in Washington drove the Bush administration to make an end run around the criminal justice system that was illegal and unnecessary."

Bush administration officials have said treating Marri as an enemy combatant who could be held indefinitely without charge was unavoidable.

"Al-Marri rejected numerous offers to improve his lot by cooperating with the FBI and providing information," wrote former attorney general John D. Ashcroft in his book "Never Again: Securing America and Restoring Justice." "He insisted on becoming a 'hard case.' "