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The inspector general reviewed but did not open a formal investigation into Maj. Weirick’s charge of unlawful command influence. A congressional source said the inspector general decided the military judge presiding over the case had jurisdiction.

In the end, the judge was taken out of play. The Marine Corps suddenly dropped the criminal charges against Capt. Clement, which headed off a trial at which defense attorneys planned to call Gen. Amos as a witness.

The Navy is honorably discharging Capt. Clement on a charge of failing to supervise the snipers. Capt. Clement has denied wrongdoing, saying he learned of the desecration only after it happened.

Maj. Weirick has garnered some allies in Congress, where Gen. Amos appears to remain popular. Several former military judge advocates wrote a joint letter asking the Senate and House Armed Services committees to investigate Gen. Amos, but no such probe is apparently underway.

The case also has put the top brass in opposing corners.

Marine Lt. Gen. Thomas Waldhauser, who originally oversaw the urination investigation, told Capt. Clement’s defense team that Gen. Amos gave him the unusual order to “crush” the eight defendants and kick them out of the Corps. He said he refused.

Gen. Amos later replaced Gen. Waldhauser, and his replacement dropped the charges against Capt. Clement.

In February, Gen. Amos broke his silence and told National Public Radio that he did not make those remarks during a one-on-one meeting with Gen. Waldhauser in February 2012.

Gen. Amos told NPR: “I have never, ever, said that I wanted them crushed and kicked out. I don’t recall at all saying that. What I do recall is there was some motivation on my part — without getting into the exact matters of the meeting — there was some motivation on my part that I questioned some early decisions by the commander. And once I left that meeting, I went, ‘OK. That probably wasn’t the right thing to do [as it] relates to undue — what we call undue command influence, the influence that a commander, a senior commander can have on the junior commander.’

“And so immediately, to correct that, I moved that case to another three-star general, and then I stayed completely out of it.”

Three months after he removed Gen. Waldhauser, Gen. Amos signed off on a memo from a three-star general outlining how he intended to dispose of cases in the urination investigation. The memo was obtained by Capt. Clement’s defense attorneys.