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Maj. Weirick considered the blanket classification illegal. He watched all this unfold as Capt. Clement was nearing a court-martial on a charge of dereliction of duty for not supervising his men.

The captain said he had no knowledge of plans to urinate on corpses or make the video. He denies any wrongdoing.

Maj. Weirick decided to take the step of filing a whistleblower’s complaint with the Defense Department’s inspector general against the commandant. The inspector general’s senior officer’s division has been conducting an inquiry.

“This incident involves the attempted, and in many ways, successful unlawful command influence by Gen. Amos to influence the outcome of cases involving Marines accused of urinating on human remains in Afghanistan,” Maj. Weirick told the inspector general.

As a pretrial hearing was to begin Sept. 11 and Capt. Clement’s attorneys were set to call witnesses to describe Gen. Amos‘ intervention, a new convening authority suddenly dropped all criminal charges. Lt. Gen. Kenneth J. Glueck had replaced Gen. Mills, who had assumed another command.

A spokesman said Gen. Glueck reviewed the case and decided it did not merit criminal charges. Defense attorneys say the action avoided embarrassing the commandant during hearings that would focus on his actions.

Gen. Glueck ordered an administrative board of inquiry, set to meet Oct. 15, to decide whether Capt. Clement should be retained or separated from the Corps.

John M. Dowd, Capt. Clement’s lead civilian attorney, said that to this day Marine prosecutors are denying defense requests for witness statements because they are classified.

Charles Gittins, a former Marine officer who practiced military law and who has been following the case, said one email to a potential witness asking him to “come clean” is not harassment.

“The Marine Corps is an embarrassment,” Mr. Gittins said. “Shoot the messenger. They have real problems with violations of law and regulation and unethical conduct at the most senior levels, which continue to be unaddressed, so they choose to go after the whistleblower. Typical. The lack of moral courage and ethics at the senior-most levels of the Marine Corps is breathtaking.”