Khan has always been a bit of an anomaly among the CIA’s so-called “ghost prisoners” who were subjected to “enhanced interrogation techniques.” His parents live in suburban Baltimore, where they moved the family in the ’90s and became legal residents. Khan graduated from Owings Mills High School in 1999 and went back to Pakistan after the 9/11 attacks over the objections of his parents, who hid his passport.

Pakistani security forces arrested him in 2003. FBI agents searched the family’s Baltimore house and trailed them for a time. The family heard no news of their son until September 2006 when President George W. Bush announced that “a terrorist named Majid Khan” was in custody and had confessed under interrogation to delivering “$50,000 to individuals working for a suspected terrorist leader named Hambali, the leader of al Qaeda’s Southeast Asian affiliate.”

A year later, defense attorneys filed a brief in federal court declaring him a torture victim of the CIA’s enhanced interrogation program. “Khan admitted anything his interrogators demanded of him,” his lawyers wrote, “regardless of the truth, in order to end his suffering.”

According to transcripts, Khan told a military board in April 2007 that he emerged from CIA custody so despairing of his isolation that he tried to kill himself by chewing through an artery in his arm.

Only six of the 779 captives who’ve been held at Guantánamo have gone before the war court. And three of them pleaded guilty after Hicks to get a shot at speedy release. Canadian Omar Khadr, 25, should have left in October, a year after he admitted to hurling a grenade that killed a U.S. solider in a July 2002 raid on a suspected al Qaida compound in Afghanistan. Khadr was 15 in 2002 and was all along spared the possibility of a capital charge because of his age. But Canadian and U.S. officials have yet to orchestrate his return, for one to seven more years in Canadian detention.

Two Sudanese men who served as al Qaida recruits have deals to finish their sentences in Obama’s second term, should he receive one.

But the case of Khan is following a far different script that sources say is taking a page from the federal court system: His sentencing hearing will come much later — after four years of testimony in other war court trials — at which time his lawyers can argue for leniency and invoke his treatment in CIA custody, which they have argued in federal court filings was torture.

Much of the Khan case is being played out in secret. The timeline of the deal itself was posted under seal last week at the Pentagon’s war court website. Military sources say Khan has been moved to a new, maximum security lockup that was set up out of public view. Where is it? That’s a secret. How much did it cost? No comment. When was it built? Ditto.

Details of the plea agreement leaked first to The Washington Post last week. The Miami Herald got the details from U.S. officials only willing to speak on background, with no name or title attached.

A Pentagon spokesman, Army Lt. Col. Todd Breasseale, would say only that Khan is secure, and unlike during the three years he spent with the CIA, his attorneys and Red Cross delegates will be allowed to see him. “We treat all detainees with the same level of dignity and respect that is due any human being.”

Khan is pleading guilty after nearly a decade in detention — interrogation without charge, isolation, and, according to his 2007 federal lawsuit, subjected to “a sophisticated, refined program of torture operating with impunity outside the boundaries of any domestic or international law” at the CIA’s secret overseas lockups, called dark sites.

His lawyers will be allowed to bring this up at sentencing, according to sources familiar with the Khan deal, in a plea for leniency. But first, says retired Navy Lt. Cmdr. Charlie Swift, a veteran of the war court, expect defense lawyers to try to use Khan’s CIA treatment whenever he’s brought as a government witness, to challenge the credibility of his testimony.

“The way you avoid the door to the dark sites is you don’t use the material,” said Swift, who challenged George W. Bush’s military commissions at the U.S. Supreme Court, and won. “But in the end they can’t avoid it. They wouldn’t know he was a potential witness unless they tortured him.”

Khan wasn’t waterboarded or subjected to “any of the other really bad techniques,” said Davis, the prosecutor who quit in October 2007 to protest senior Pentagon interference in what should be independent prosecutorial decision making.

But he said, “It’s hard to put a good spin on somebody spending more than a decade in confinement waiting for their day in court. I don’t know how you clean that up.”