Lt. Col. Leonard Grado was stunned when Army lawyers came knocking in 2014, intent on putting him in prison for sexual misconduct charges he thought had been resolved half a decade before.

“Was I aware of the witch hunt going on?” Grado asked. “I am now.”

Ever since the case against him had been dropped, a rising political clamor over sexual assault in the ranks had forced the Pentagon to aggressively confront the problem, which critics contend top brass ignored or downplayed for years. Grado’s case was reopened as commanders second-guessed lower-level decisions to dismiss cases like his. But this process created another problem: the erosion of due-process rights for the accused.

Military attorneys, criminal investigators and administrative experts say new procedures implemented in recent years have curtailed defendants’ rights to cross-examine witnesses, conduct discovery and present evidence. Commanding officers have been stripped of their ability to dismiss charges they deem dubious or unfounded.

As a result, the atmosphere in the armed services regarding sexual assault has come to resemble the more publicized one on college campuses, where critics say bedrock principles of American justice, most notably the presumption of innocence, are being given short shrift.

Pentagon officials disagree. They say their enhanced focus on sexual assault has produced measurable results, reducing the number of service members who experienced “unwanted sexual contact” while increasing the confidence of accusers that their complaints will be taken seriously and they will not suffer reprisals.

The Pentagon’s spokesman on sexual assault, Johnny Michael, maintains that reforms like the Military Justice Act of 2016 “further enhanced the rights of both accused service members and the victims of alleged offenses at courts-martial and on appeal.”

It’s a view not shared by those involved with defending accused service members.

“Every change they’ve made since 2005 was to the disadvantage of the accused,” said former military defense attorney Charles Gittins. “It got worse as time went on.”

A graduate of the Naval Academy at Annapolis, Gittens abandoned military legal defense work in 2012 after handling the sex-assault cases of some 100 service members. The Uniform Code of Military Justice has been stripped of “any bulwark against baseless charges,” he concluded.

“The victims now control investigations, and that’s the biggest enemy within the rule of justice,” said Carolyn Martin, a private investigator who works for the defense on military cases. “So many politicians are coming out with this belief the victim is always right. Are you kidding me? We’re talking about the Constitution of the United States. There is presumed innocence, but now the deck is stacked against the accused.”

Given the vagaries of sexual assault, statistics are imprecise and subject to interpretation. The advocacy group Protect Our Defenders highlights an anonymous survey the Pentagon conducts biennially in which 20,300 service members reported that they had been sexually assaulted in 2014, the most recent year for which the figures have been compiled. The group also notes that the 4,744 formal complaints actually filed in 2014 represents just a quarter of those incidents and that only a fraction of those resulted in actual courts-martial. The group said such discrepancies reflect the widespread belief among service members that their claims will not be thoroughly investigated and could even result in backlash against victims.

Leonard Grado, on duty south of Baghdad in 2003, attends to an Iraqi man wounded by shrapnel.

The Pentagon argues that a series of 54 initiatives enacted since 2012, under the rubric “Sexual Assault Prevention and Response” (SARP), has reduced sexual assaults while building confidence that top brass will take complaints seriously. Between 2012 and 2014, for example, the survey numbers dropped (to 20,300 from 26,000) while the number of formal complaints rose (to 4,774 from 2,828).

“Fewer sexual assaults are occurring in the military, while more service members are choosing to report the crime,” is how Michael, the Pentagon spokesman, explained the figures. Yet such numbers are scant consolation to those who feel their lives have been upended for purposes of political expediency.

Leonard Grado’s odyssey through the military justice system began in November 2009. He was a doctor of osteopathic medicine stationed at Fort Campbell, Ky., after 10 years of unblemished duty, including deployments to Bosnia, Iraq and Afghanistan. The civilian wife of a soldier came to him for an examination, complaining, she later testified, of general pain “all over, like in my stomach, in my chest, having headaches.” Grado began, she said, by checking her scarring from breast reduction surgery. Eventually he asked her to disrobe and touched her genitalia – an account Grado denied.

Distressed over the examination, she later called “my sister or one of my friends,” who urged her to file a complaint that she had been molested – even though, as she testified, “I didn’t think that I was.”

“It was the first time I ever saw this patient,” Grado said. “There was no indication of anything abnormal. She made a follow-up appointment.”

The Army launched two proceedings: a “command investigation,” or an AR 15-6; and, as required by new rules regarding sexual assault claims, an inquiry by the Army’s Criminal Investigation Division. Grado said he gave a statement voluntarily. Those investigations turned up no evidence supporting the complaint. The Army never limited his medical privileges. By late spring 2010, “I and my hospital command figured it was over.”

It wasn’t. That year a colonel he had never met had placed into his file a document that would stop his military career in its tracks – put there based on the woman’s complaint alone. It was a General Officer Memorandum of Reprimand, a so-called “GOMOR,” which is widely considered a bar to future promotion.

Fast forward to 2014, when the military lawyers showed up at his later posting at Fort Lewis, Wash., informing him that higher-ups now wanted to pursue the case. In this shrouded process, he would never learn who those superiors were.

Grado hired his own lawyer, Jocelyn C. Stewart. She said the first chance they had to question his accuser was at a preliminary hearing in March 2014, when the Army had set a court-martial in motion. The woman, who could not be reached for comment, got prerogatives unavailable to him. She was “accorded an advocate under the Army’s Special Victims Counsel Program and a plethora of free services,” Stewart said.

As the Pentagon spokesman noted, these services were part of the military’s evolving approach to sexual assault allegations, which intensified in 2012 “when the secretary of defense began to focus intensely on this problem.”

At the same time, Congress, spurred by Democratic Sens. Kirsten Gillibrand of New York and Claire McCaskill of Missouri, began limiting protections for the accused in the military, according to several attorneys and experts involved in defending such cases.

Some changes were made to the Uniform Code of Military Justice, but many more came through tweaks to National Defense Authorizations – legislation through which the Pentagon is funded. The changes allowed appeals to impose sentences harsher than those meted out in military tribunals, Stewart said.

A spokesman for Gillibrand declined to comment and McCaskill’s office never replied to questions RealClearInvestigations submitted in writing at its request. The two senators do not always move in concert on the issue; Gillibrand, for instance, would like sexual assault cases removed entirely from the military chain of command while McCaskill is more supportive of the Pentagon’s efforts to combat the problem.

All of the changes, which included stripping commanders of their authority to dismiss guilty verdicts that they found based on dubious evidence or proceedings, have tilted the scales of justice against the accused, critics say. They have also created incentives for politically attuned commanders to push flimsy or marginal cases toward a court-martial instead of accepting initial recommendations that they be dropped.

That’s what happened to Marine Capt. Nicholas Stewart. More than a year after he partied and then slept with a friend with whom he had previously been intimate, he was charged after word of the encounter got back to the woman’s parents and they complained to the Marine Corps. Stewart was convicted of sexual assault in 2009.

The case hinged on a rule change – the military had decided in 2006 that if a person was “substantially incapacitated by alcohol” then consent could not be given and a crime had occurred. The alleged victim had sent Stewart an e-mail saying, “I can’t even say I told you ‘no,’” and Judge Advocate General officials concluded there was no case, but the rule change and the political winds meant Stewart was in trouble anyway, according to his lawyer, Charles Gittins.

Even at trial, Stewart fell victim to this more zealous atmosphere. The jurors acquitted him of one crime, but the judge then ordered them to deliberate over a nearly identical-sounding charge, and on that he was convicted. He served nearly half of a two-year sentence before an appeals court vacated it in 2012, ruling that the verdict raised fundamental due-process concerns involving double jeopardy. Stewart, who declined to comment when approached by RealClearInvestigations, has returned to active duty.

“I would characterize his case as a product of the politics of fear of sexual assault by senior officer leadership,” Gittins said. “No convening authorities want to be labeled as weak on sexual assault, so the [convening authorities] sent it to trial.”

That fear is widespread among commanding officers, according to experts. John Wells, a retired Navy commander and now the executive director of Military-Veterans Advocacy Inc., said he has handled roughly a dozen cases involving sexual allegations and that in “100 percent” of them his clients’ due-process rights have been violated.

In 2009, Wells managed to clear Sam Harris and Roger House, two Navy officers accused of having raped a service woman in a case that, like Stewart’s, investigators initially recommended be dismissed. Instead, Rear Adm. George E. Voelker overruled the Judge Advocate General and ordered that the men face a court-martial.

“Generals and admirals are scared to death,” Wells said. “Sexual assault is a problem; it does exist, but my concern has been the tinkering might make it easier to get a conviction, but not for getting justice.”

At his court-martial in 2014, Grado faced 30 to 40 years behind bars if convicted of all of the counts of sexual misconduct against him – ones he thought had been dropped as baseless long ago. With a defense team comprised of Jocelyn Stewart and a military lawyer he got after being formally charged, Grado said he was “able to present a defense for the first time.”

The trial lasted four days. His defense hinged on inconsistencies in the accuser’s account; a lack of corroborating evidence; and a thorough investigation of Grado’s past that had turned up nothing. The jury acquitted Grado on every charge after two hours of deliberation.

“The prosecutor literally cried when I got acquitted – that’s how much they are invested in it,” he said. “They wanted my scalp – they wanted a scalp, and I was a high-ranking one.

“I really did feel like my life was getting turned upside down. A woman can just say this and then, if it weren’t for some courageous officers at my court-martial, I could have been in Leavenworth.”