The Army owes Captain James Yee, a Muslim Army Chaplain who was arrested on Sept. 10, 2003, an apology and an explanation. Last year, officials at a Naval Air Station in Jacksonville, Florida discovered allegedly classified documents in Yee’s bags. At the time of his arrest, Yee was serving in Guantanamo Bay, Cuba, where he ministered to prisoners at the Navy’s detention facility. He ensured that the prisoners were able to hear the Muslim call to prayer, and occasionally clashed with military officials over the treatment of Islamic detainees.

Yee was accused of espionage, sedition, mutiny and aiding the enemy (crimes punishable by death). He sat in solitary confinement for 76 days after his arrest while Defense Department officials anonymously pressed their case in the national media, portraying Yee as part of a Guantanamo spy ring that sympathized with Al Qaeda, and raising suspicions that Yee had passed military secrets to the Syrians. “The fear was that he had started mixing his loyalties,” one official told the Washington Post.

Another official explained Yee’s decision to become a spy this way: “He was disappointed that he wasn’t being integrated into the interrogation process. He wasn’t happy with the mission, and thought the detainees were being mistreated.” (At the time, Yee’s concerns about conditions at Guantanamo Bay were echoed repeatedly by human rights activists.)

All allegations against Yee were eventually dismissed. But then, in a decision that can only be characterized as outrageous overreaching, the Army decided to prosecute Yee for committing adultery and downloading porn onto his computer. Neither act is a criminal offense, and the move was widely regarded as vindictive because, traditionally, the only times when the military prosecutes adultery cases is when other charges like rape or sexual harassment are also involved.

Yee received a reprimand, but a month later, an Army general threw out even this judgment. Exonerated on all charges, Yee received word last week that the Army had authorized his honorable discharge, which is now set for January.

Experts in military justice have expressed disbelief at Yee’s Kafkaesque journey from well-regarded Army Chaplain to Public Enemy No. 1. The malice exhibited towards Yee and the Army’s incompetent handling of his case are staggering. “This whole thing makes the military prosecutors look ridiculous,” John L. Fugh, a retired major general and onetime judge advocate general (the highest uniformed legal officer in the Army), told the New York Times.

The military owes Yee an apology because it dragged his name through the mud, damaged his family and destroyed his reputation. Yee said the Army’s pursuit of the case against him has “irreparably injured my personal and professional reputation and destroyed my prospects for a career in the US Army.”

But an explanation must also be forthcoming. “The notion that you would keep an officer in maximum security based on these charges is preposterous,” Yee’s civilian lawyer, Eugene Fidell, said while Yee was sitting in solitary confinement. The Army must explain why Yee was held in such primitive conditions on trumped-up charges.

It’s also fair to ask whether Yee’s questions about prisoner abuses put him in the crosshairs of Major General Geoffrey Miller.

Miller, who is a central figure in Sy Hersh’s new book, Chain of Command, had been in charge of the Guantanamo Bay prison, where he brought a no-holds barred attitude to the interrogation process that created a climate of fear in which abuses were condoned. “Miller was permitted to use legally questionable interrogation techniques at Guantanamo, which could include, with approval, sleep deprivation, exposure to extremes of cold and heat, and placing prisoners in ‘stress positions’ for agonizing lengths of time,” Hersh reported.

It was Miller, according to the US Southern Command, who made the major decisions about how to handle Yee’s case, including deciding to bring the initial charges against him, to have him detained in the brig and to include the additional charges.

Miller may well have seen Yee as a threat to his mission to interrogate prisoners freely and without dissent. During his stint in Guantanamo, Miller was dispatched to Iraq to “Gitmoize” prisoner interrogations, where Miller’s team, according to the report by Army Maj. Gen. Antonio Taguba, insisted that “the guard force be actively engaged in setting the condition for the successful exploitation of internees.” When asked about Miller, Fidell said: “It is incomprehensible that General Miller would have been put in charge of Iraqi prisoners given his conduct in [the Yee] case.”

Former counter-terrorism officials have pointed out that military commanders responsible for abuses were instructed to “[take] off the gloves” to glean better intelligence from prisoners. Yee was caught up in this “gloves-are-off” atmosphere. A kind of hysteria surrounded his case, and his treatment may well have been a result of his warnings about abuse of detainees. In prosecuting its case against Yee, the Army trampled on the values that underpin American ideas about fair play and equal justice for all.

Moreover, as David Cole pointed out in a recent Nation article, it is a record of prosecutorial abuse and failure: John Ashcroft has compiled a 0 for 5,000 record when it comes to successfully prosecuting foreign nationals the government has detained on suspicion of sponsoring terrorism.

“Yee was defamed and smeared and accused of being a spy,” said Ibrahim Hooper, a spokesman for the Council on American-Islamic Relations. Now that the case against Yee has disintegrated, it seems plausible, in retrospect, that Yee’s only real crime in the brass’ eyes was his willingness to raise questions about abuse of prisoners when few in the military, the media and the federal government had the wisdom to do so. Yee deserves better.