After he learned that one of his fighter pilots had been convicted of sexual assault in a military court, Air Force Lt. Gen. Craig Franklin sent an email with a single question:

“Does he receive his retirement?”

The pilot, Lt. Col. James Wilkerson, had been convicted by a four-panel jury of ranking officers of aggravated sexual assault of a woman who was staying in his home. They sentenced him to a year in prison and dismissal from the Air Force.

Under military law, all convictions must be reviewed by a top official, who has the power to uphold or overturn them. In Wilkerson’s case, that official was Lt. Gen. Franklin.

The service member who responded to Franklin’s email, written less than an hour after he learned of the conviction, explained that the lieutenant general would have final action on the sentence. “If the dismissal is approved, he will not be eligible for retirement,” the email said.

“Copy,” Franklin responded.

Four months later, in February this year, Franklin overturned the sentence, reinstated Wilkerson in the Air Force and even tried to get him a promotion. His emails show that Franklin personally reached out to Wilkerson to offer him advice and consult with him on what he’d like to do next in his career.

The emails, released by the Air Force late last week through a Freedom of Information request, offer new insight into the decision-making process behind a case that has drawn the attention of members of Congress and sparked a debate on how the military addresses sexual assault.

The Military’s Sexual Assault Problem

The military’s long struggle to deal with sexual assault has its roots in the culture of the military leadership, according to victims’ advocates and former service men and women who have been assaulted.

Most sexual assault crimes never make it up the chain of command to a court-martial, according to the Pentagon’s own data.  A Pentagon survey released earlier this year estimated that 26,000 service members had experienced “unwanted sexual contact” — which includes rape, attempted rape and unwanted sexual touching — but only 3,374, or 13 percent, reported the incidents. There were only 302 prosecutions.

A full 50 percent of servicewomen who were victims of assault said they didn’t report it because they believed nothing would be done.

Service members can silence victims or retaliate against them long before a report reaches a commanding officer, explained Capt. Lory Manning, a retired Navy commander who now heads the Women in the Military project at the Women’s Research and Education Institute.

In the military, reports of sexual assault in a unit reflect poorly on supervisors, because it shows they can’t discipline their unit. That makes it more likely for junior supervisors to discourage reporting up the chain of command and even to retaliate against the victim, Manning said.

“Suddenly [the victim] is the one on duty on Christmas Day, who can never have a day off, or go on leave,” she said. Service men and women all understand this, victims’ advocates say, so they keep quiet.

“In Cases Like This, Support for the Child Is Often a Concern”

Once cases do get reported, most commanding officers do their best to see justice done, Manning said. But sexual assault cases can be complex, and if an officer knows the accused, it can be difficult to be impartial, she said. Service members convicted of a felony are dishonorably discharged, and face the loss of their health care, pension and other military benefits.

“You know somebody, you know his good work, you know their wife, their kids — and the consequences not only to them but to the wife and kids if the guy is found guilty of a felony,” she said.

“Too often they bend over backwards to be more than fair to the accused, and they don’t worry so much about the victim.”

The nation’s top military official recently concurred.

“You might argue that we have become a little too forgiving,” Gen. Martin Dempsey, the chairman of the Joint Chiefs of Staff, said in May about sexual assault. “If a perpetrator shows up at a court-martial with a rack of ribbons and has four deployments and a Purple Heart, there is certainly the risk that we might be a little too forgiving of that particular crime.”

In the Wilkerson case, the pilot’s direct supervisor, Brig. Gen. Scott Zobrist, wrote to Franklin that he hoped the commanding officer would uphold the conviction. Returning Wilkerson to active duty on the Aviano Air Force Base would be “absolutely devastating in so many ways that I cannot even begin to consider it,” he said, citing morale on the base, as well as the broader message the move would send to service members and the victim.

Zobrist also indicated his concern that Franklin might be considering other factors apart from the trial evidence in his review.

“I know in cases like this, support for the child is often a concern…” he wrote, referring to Wilkerson’s young child. “I’m concerned that a desire to help [the child] by possibly reversing the dismissal will have major second and third order consequences.”

Franklin responded with a short line the same day: “Copy all below. Appreciate the input.”

Franklin would later defend his decision to overturn Wilkerson’s conviction in a letter in March, saying he conducted an “exhaustive and complete” review of the evidence before making a decision, including 91 letters of support from Wilkerson’s family and friends, some of which he read “several times.” Franklin added that accusations he didn’t take sexual assault seriously are “complete and utter nonsense.” He didn’t immediately respond to an email seeking a comment.

Franklin’s superiors, Gen. Philip Breedlove, and Gen. Mark Welsh, who was at the time the top Air Force commander in Europe, emailed their support. “I think it was the right thing to do, but it’s going to be a little uncomfortable for awhile,” wrote Welsh, who has since been promoted to Air Force chief of staff. “Hang in there — good time to be in Europe!”*

None of them mentioned the victim.

“I Am So Upset About This”

The Wilkerson case sparked public outrage and led to congressional hearings on sexual assault in the military. Sen. Claire McCaskill (D-Mo.) requested a formal review of Franklin’s decision.

“My heart is beating fast right now, I am so upset about this,” she said at a March hearing about the case. “I question now whether that unit that man returns to, whether there’s any chance a woman who is sexually assaulted in that unit would ever say a word. What that general just said is that that jury’s decision didn’t matter.”

During several congressional hearings, military officials argued to keep decisions about prosecuting sexual assault within the chain of command, saying that it would undermine military order and deprive commanders of a powerful tool in maintaining order among their troops.

But following the hearings, two bills were introduced in the Senate to prohibit commanders from overturning jury convictions and criminalizing retaliation against victims who report sexual assault, among other reforms.

One of the bills, backed by McCaskill and Carl Levin (D-Mich.), would also require an automatic review by a civilian when a commander disagrees with a legal counsel’s recommendation. It was approved by the Armed Services Committee and should come up for a vote towards the end of the year.

Sen. Kirsten Gillibrand (D-N.Y.), has proposed an alternative bill to remove the decision on whether to convene a court-martial for sexual assaults and other serious crimes from the chain of command, allowing military prosecutors to decide on whether to bring a case.

The committee didn’t accept that provision, but Gillibrand plans to reintroduce it as an amendment to the McCaskill-Levin bill, according to Glen Caplin, her communications director, when it finally comes to the Senate floor.

“It’s just a common-sense, practical proposal that legal decisions over whether a case should go to trial should be in hands of trained military prosecutors and not commanders,” Caplin said.

It’s unlikely the legislation will be put up for a vote until later this year.

McCaskill, in a statement, told FRONTLINE that the emails “should disgust” military members serious about change, and highlight the need to strip commanders of the ability to overturn convictions. “I’ll keep fighting for this reform, alongside the many others included in the defense bills, to ensure that the miscarriage of justice that occurred in the Aviano case never happens again,” she said.

*[Update 9/5: Welsh’s public affairs advisor Maj. Megan Schafer called to clarify the general’s email to Franklin. She said that Welsh told her that his email was intended to express support for Franklin’s letter explaining the decision, not the decision itself. “That email can be taken in two ways,” she said. “What he meant was,  ‘I agree with your decision to write about this.'” According to Schafer, Welsh wouldn’t publicly express his opinion on the overturned verdict because Franklin was the convening authority in that case.]

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