A military judge did something extraordinary last summer when he ordered the Marine Corps‘ top officer to submit sworn statements in a sexual assault case.

The answers from the commandant, Gen. James F. Amos, have some in Marine legal circles wondering whether he told the full truth.

Gen. Amos, a Joint Chiefs of Staff member, faces charges from defense attorneys that his words and actions have unleashed a wave of unlawful command influence over jurors who venerate the commandant.

A fellow general said the commandant ordered him to “crush” Marine defendants in the desecration cases of those caught on videotape urinating on Taliban corpses. Defense attorneys call that order blatant, illegal command interference.

The Defense Department inspector general has begun an investigation of Gen. Amos based on a whistleblower complaint filed by Maj. James Weirick, a staff attorney at the Marine base at Quantico, Va., who saw what he considered illegal interference. IG investigators have interviewed Maj. Weirick and several senior generals.

A Marine spokesman said the commandant denies any wrongdoing, is committed to giving defendants fair treatment and looks forward to litigating the charges in court.

Gen. Amos‘ sworn statement was given in a sexual assault case. But military defense attorneys across the country are trying to get a variety of charges dismissed against their clients, citing public statements from Gen. Amos, administration officials and President Obama to assert that their clients cannot get a fair trial.

In signed and sworn answers to defense attorneys’ questions on July 31, 2012, Gen. Amos told a military judge that he did not intervene in cases in which he delivered a series a speeches on moral conduct and the need to punish wrongdoers.

“At no time did I directly or indirectly intend to dictate any course of action in any particular case or type of cases,” he said in the statement.

Switching investigators

Six months earlier, he ordered Marine Lt. Gen. Thomas D. Waldhauser, in a one-on-one meeting in the Middle East, to “crush” the defendants in the urination case and make sure some of them were court-martialed, according to Gen. Waldhauser.

“The fact that the military judge ordered the commandant to answer written interrogatories is pretty amazing. That happens rarely,” said Charles Gittins, a former military defense counsel. “But now he has a bigger problem: His statement in the interrogatories is false. And he had to know it was when he signed the thing. Amazing bit of hubris.”

At the time of the meeting, Gen. Waldhauser oversaw the desecration investigation in his job as what is called the convening authority. The post, by law, is supposed to be independent of superiors to make sure the accused are treated fairly.

Gen. Waldhauser is now Defense Secretary Chuck Hagel’s senior military assistant and is soon to take a job as a staff director for the chairman of the Joint Chiefs.

Washington was jarred in January 2012 when a YouTube video showed four Marine snipers urinating on the corpses of Taliban fighters they had killed.

Obama administration officials, sensitive to Muslim outrage, condemned the conduct. Gen. Amos ordered an investigation and named Gen. Waldhauser, then in charge of U.S. Central Command Marines, to oversee judicial cases for more than a half-dozen defendants.

The next month, Gen. Amos met one-on-one with Gen. Waldhauser overseas.

The public now knows about this secret meeting because attorneys for Capt. James Clement, who is charged with conduct unbecoming an officer for failing to supervise his men more closely, filed details in court Tuesday. The filing was first reported by Marine Corps Times.

It is part of a motion to dismiss charges because of what attorneys say was Gen. Amos‘ unlawful command influence.

“The investigations, dispositions and prosecutions of the alleged desecration of corpses by U.S. Marines in Afghanistan have been fatally infected by [Gen. Amos‘] unlawful control from January 2012 to the present day,” the attorneys wrote. They are Marine Maj. Joseph Grimm and John Dowd of the Washington law firm Akin Gump Strauss Hauer & Field, who took the case pro bono.

Gen. Waldhauser, in a written declaration, said the investigation was months away from being completed, so he expected his session with Gen. Amos to be simply an update.

“I do not necessarily remember the exact words or sequence of what was said, but the [commandant] did make a comment to the effect that the Marines involved needed to be ‘crushed,’” Gen. Waldhauser said. “The [commandant] went on to say that he wanted these Marines to be discharged from the Marine Corps when this was all over.”

Gen. Waldhauser said he was considering a range of actions, from nonjudicial punishment to more serious charges that would mandate a court-martial. He said he could not guarantee that the Marines would be discharged, as the commandant wanted.

Gen. Amos said: “Why not, or will you give them general court-martials?” — which could result in what amounts to felony convictions.

“No, I am not going to do that,” Gen. Waldhauser said.

Gen. Amos then reminded Gen. Waldhauser that he had the power to fire him.

Gen. Waldhauser, while on a layover in Europe, received a call from the assistant commandant, Gen. Joseph F. Dunford Jr., who is now the top commander in Afghanistan. Gen. Dunford said Gen. Amos regretted what he had said, but because he had said it, he was forced to remove Gen. Waldhauser as the convening authority.

“I had never [before] been removed as the convening authority of a case,” Gen. Waldhauser said.

Gen. Amos appointed Lt. Gen. Richard P. Mills, who heads Marine Combat Development Command in Quantico, to replace Gen. Waldhauser.

In his own words

The dust-up was kept secret. Marine Corps Times reported that it had been misled by Marine headquarters: When a reporter asked in 2012 why Gen. Waldhauser was replaced, the response was that he was preparing for his job with the defense secretary.

Capt. Clement’s attorneys said the replacement was a “ruse and an excuse” by Gen. Amos so that he could appoint an overseer who would adhere to how he wanted the cases to be handled.

The attorneys filed a memo from another general, the defendants’ commanding general at Camp Lejeune, N.C. He wrote to Gen. Amos in May 2012 seeking approval for how he planned to dispose of some of the desecration cases. Gen. Amos initialed his approval.

“That is not normal procedure,” said Mr. Gittins, a former Marine aviator as well as defense counsel.

Capt. Clement’s attorneys cite a series of examples of Gen. Amos committing unlawful command influence, such as his order to Gen. Waldhauser to “crush” the defendants and his “Heritage Tour” in the spring and summer of 2012, when he delivered several speeches urging commanders to punish and rid the Corps of wrongdoers. He cited the urination case, in which trials were still pending.

Defense attorneys quoted him saying on May 23, 2012, at Camp Pendleton, Calif.: “My lawyers don’t want me to talk about this, but I’m going to anyway. The defense lawyers love when I talk about this, because then they can throw me under the bus later on and complain about unlawful command influence.”

Gen. Amos said in his sworn statement: “As the commandant, I must address difficult topics, and I have advisers who help me do that while staying within the bounds of the rules.”

Capt. Clement’s attorneys said Gen. Mills, once he relieved Gen. Waldhauser, had a duty to disclose why he was the new convening authority, but he did not. A Marine Corps spokesman said Gen. Mills did not know why Gen. Amos replaced Gen. Waldhauser.

The same month he fired Gen. Waldhauser, Gen. Amos ordered the entire urination case classified as secret, making it more difficult for attorneys to obtain evidence or the communications between the overseeing generals. The defense court filing said Gen. Amos was so involved in Gen. Mills’ supposedly independent post that he even dictated how press releases were written.

Gen. Mills ended up charging Capt. Clement with offenses that had been dropped by prosecutors, and ignored a hearing officer recommendation that he not be court-martialed, according to the filing. His trial is scheduled for Nov. 1.

The Marine Corps agreed to release internal documents and high-level communications only after defense attorneys met with Gen. Waldhauser and learned he had been pressured by Gen. Amos.

‘Compromised the situation’

Col. Sean Gibson, a Marine Corps spokesman, issued a statement defending Gen. Amos.

Of the Amos-Waldhauser meeting, Col. Gibson said: “During that conversation, the [commandant] made some comments to Lt. Gen. Waldhauser that Gen. Amos felt could be perceived as interfering with Lt. Gen. Waldhauser’s independent and unfettered discretion to take action in those cases.

“The Commandant immediately realized that he had compromised the situation and took immediate action to ensure that the investigation and cases were given to an appropriate new convening authority who could exercise independent and unfettered discretion to take action in those cases.

“There was never any intent to manipulate the courts-martial system to undermine the rights of any Marine involved. The rights of the accused in these cases have been protected throughout every step of the military justice process.”

Col. Gibson added: “We strongly disagree with most of the factual assertions and many of the legal conclusions suggested by the accused’s pleadings. We look forward to responding and litigating this matter in court.”

A Pentagon spokesman said Gen. Waldhauser did not wish to comment.

The whistleblower complaint to the inspector general defends Gen. Mills, saying he has “at all times fulfilled his role as convening authority in an impartial manner” and that he was “put in this precarious position by those officers above him.”

Allegations of unlawful command influence against Gen. Amos is arising in other cases, including sexual assault charges against Staff. Sgt. Tarrell Jiles, who is accused of harassing and touching fellow male Marines.

Ordered to submit to defense questions in the Jiles case, Gen. Amos said of the Heritage Tour: “At no time did I directly or indirectly intend to dictate any course of action in any particular case or type of cases.”

Defense attorneys say this is less than truthful because the commandant had pressured Gen. Waldhauser and was trying to influence Gen. Mills during 2012.

Mr. Gittins said any commander who violates court procedures can be charged under Article 98 of the Uniform Code of Military Justice, the federal law that contains the armed forces’ criminal code and dictates how courts-martial should be conducted.

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