A comment by President Barack Obama on military sexual assaults — deemed “unlawful command influence” by some judges — is altering the conduct of courts-martial throughout the services, and may factor into discharges and other proceedings outside the courtroom.

The complications come in the midst of increased congressional and public scrutiny of sexual assault in the military over the past year.

That scrutiny led the president and senior military leaders to talk tough — too tough, according to legal officials who say their overly specific comments about sexual assaults violated the Uniform Code of Military Justice, tainted juries and harmed the rights of the accused.

In May, Obama told reporters that servicemembers engaging in wrongful sexual activities must be “prosecuted, stripped of their positions, court-martialed, fired, dishonorably discharged. Period.”

One month later, Hawaii military judge Cmdr. Marcus Fulton ruled in arguments before U.S. v. Petty Officer 2nd Class Ernest Johnson that Obama’s call for dishonorable discharges — one of multiple options a military jury considers when they ponder sentencing — could be interpreted as a commander-in-chief’s orders. To remedy the perceived sentencing bias, Fulton ruled that should Johnson be convicted, he cannot receive a bad-conduct or dishonorable discharge. The ruling wouldn’t keep a convicted sailor out of prison, but it could conceivably allow him to retain military and veterans benefits after serving any potential sentence.

Since that ruling, the president’s words have become a commonplace defense argument in sexual assault hearings. Attorneys for Brig. Gen. Jeffrey Sinclair, accused of unlawful sexual contact in one of the military’s most visible sex crime cases, brought up the argument during pretrial motions last month. Rulings on Obama’s comments are pending in other trials in Japan, Hawaii and the mainland United States.

After Fulton’s ruling, White House officials said Obama was listing examples of how those convicted of sexual assault could be held accountable, not intending to direct a particular result in any specific case.

Still, military trial judges, working without substantial higher court precedents, are coming to varying conclusions on whether and how Obama’s statements have damaged the rights of the accused, and what they should do about it.

In a Yokosuka Naval Base pretrial hearing for a chief petty officer accused of sexual assault July 3, military judge Cmdr. John Maksym found that Obama’s comments, as well as others by and Joint Chiefs Chairman Gen. Martin Dempsey, constituted apparent unlawful command influence.

But instead of ruling out punitive discharges, Maksym awarded the defendant five peremptory challenges, meaning his lawyers can dismiss five potential jurors without giving a reason. The military justice system normally allows each side to do this only once.

The varying verdicts and arguments could persist unless the U.S. Court of Appeals for the Armed Forces, or CAAF, receives one or more cases that are large enough in scope to set a precedent.

No one is sure if, or when, that will happen during the current presidential administration.

“Eventually, the issue will ‘burn off’ as the effect of President Obama’s comments dissipates over time,” said Eugene Fidell, who teaches military justice at Yale Law School. “There’s no way to put an end-date on it, other, perhaps, than the stroke of noon on Jan. 20, 2017.”

On Monday, the Navy-Marine Corps Court of Appeals could order oral arguments from each side regarding Fulton’s ruling. The appeals court has postponed Johnson’s trial until the issue of unlawful command influence is resolved.

Prosecutors argue that comments by Obama and other senior leaders have little impact at lower levels of the military, and that it remains unclear whether civilians are capable of unlawful command influence.

If Fulton’s ruling is allowed to stand, “it may be the final straw that undermines the public’s faith in the fairness of the military justice system,” Marine Corps Maj. Paul Ervasti wrote in the government’s petition to the appeals court.

Defense attorneys — and in this case, Fulton — agree that public faith in the military justice system is at stake. They state that the generals and admirals who convene courts-martial could feel pressured to approve specific sentences, and pressure will flow downward toward judges and juries.

“A member of the public who is aware of all the facts and circumstances in this case would have doubts whether the accused would receive a post-trial review … untainted by improper external influences,” Fulton wrote in the June ruling.

If the service appeals court validates Fulton’s ruling, it’s difficult to know whether it would be appealed.

Like many higher appeals courts, CAAF accepts only a fraction of the appeals it receives. However, there are signs that the court is interested in the larger issue.

On June 27, CAAF set aside the unpremeditated murder conviction of Marine Sgt. Paul Hutchins III on the grounds that investigators acted improperly.

That conclusion mooted a second question — whether Secretary of the Navy Ray Mabus’ comments that Hutchins’ act was “so completely premeditated,” and that Hutchins had been granted “substantial clemency already,” constituted unlawful command influence.

Chief Judge James E. Baker wrote that “by failing to address the allegations of unlawful command influence, the majority avoids a systemically important question and central aspect of the case, which warrants inquiry and consideration by this Court.”

Judge Margaret Ryan called Mabus’ comments “disturbing and inappropriate.”

Even if CAAF sets a clear precedent, it would only settle courtroom matters.

Clemency and parole boards, as well as servicemember discharge boards, are also composed of military personnel.

Servicemembers facing extended jail time or undesirable discharges could argue that the boards have been influenced by senior leader comments. However, even the military’s highest appeals court has no jurisdiction over such boards.

“This means the president’s comments could eventually come under scrutiny in the federal courts,” Fidell said. Twitter: @eslavin_stripes

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