The Muslim chaplain who once was accused of mishandling classified material and other charges, only to have the case against him fall apart, said yesterday that he is resigning from the Army.

Capt. James J. Yee, who was arrested while posted to the military prison at Guantanamo Bay, Cuba, to minister to suspected al Qaeda and Taliban fighters held there, said the Army's handling of its case against him "irreparably injured my personal and professional reputation and destroyed my prospects for a career" in the Army.

Yee, a 1990 graduate of West Point, said in a statement released by his lawyer that he had asked to be discharged next January.

Yee was arrested after several hours of interrogation on Sept. 10, 2003, at the Naval Air Station in Jacksonville, Fla., after flying from the Guantanamo Bay Navy base, where he had been assigned for the previous 10 months. The next month he was charged with mishandling classified information after authorities found maps of the Guantanamo prison and information about detainees in his possession. FBI and Defense Department officials indicated that they were investigating whether Yee also had committed more serious offenses, and court documents included a variety of serious accusations of espionage. Yee was held in solitary confinement at the Navy brig in Charleston, S.C., for more than two months.

But the case against Yee soon began to fall apart. Eventually the military dropped all criminal charges against him, but it still pursued accusations growing out of the investigation that he had committed adultery and stored pornographic images on a government computer. He was reprimanded for those lesser offenses, but that ruling was thrown out on appeal.

"I have waited for months for an apology for the treatment to which I have been subjected, but none has been forthcoming," Yee said in the statement released by his attorney, Eugene R. Fidell. The Army has given no indication that it will apologize to Yee, Fidell said.

The Army had no comment on Yee's case. A spokesman for the U.S. Southern Command, which oversees the base at Guantanamo Bay, referred questions to the Army base at Fort Lewis, Wash., where Yee is now posted. An Army spokesman there said he could not comment because he had not received confirmation that Yee had submitted a letter of resignation.

Yee grew up a Lutheran in New Jersey and after graduating from West Point commanded a Patriot missile battery. He converted to Islam after serving in Saudi Arabia after the 1991 Persian Gulf War. He then left active duty and studied Islam in Syria. In the late 1990s, he rejoined the Army as a Muslim cleric.

Yee intends to finish a master's degree in international relations at Troy State University and may then pursue a doctorate, Fidell said.

"I think his case is going to resonate with people for a long time, because the basis for his 76 days of solitary confinement remains unexplained," Fidell said when asked about the impact of the case. "This case leaves you scratching your head. How could an officer be put in solitary confinement for 76 days, and then the case crumbles?"

Scott Silliman, a specialist in national security law at Duke University, essentially agreed with that summary, saying the Yee case will be remembered as an instance of the military bringing charges without adequately investigating the matter. He said he worries that such premature action may be characteristic of some military lawyers during wartime.

Capt. James J. Yee, a Muslim chaplain to detainees at Guantanamo Bay, had been arrested for taking classified materials. The charges were dropped.