SAN ANTONIO » Marine 2nd Lt. Elle Helmer woke up on a cold floor, lost and surrounded by darkness. Her body screamed with pain, her underwear had been removed and she tasted blood in her mouth. She could hear someone else in the room with her, breathing slowly.

Memories from the past few hours flashed through her mind as she crawled toward a doorway for light. On orders from her command on March 16, 2006, Helmer had joined her fellow officers for a St. Patrick’s Day pub run, a night of bar-hopping that ended across the street from the prestigious Marine Barracks Washington, where she was in charge of public affairs.

A major followed Helmer out of the last bar and summoned the petite 25-year-old to his office, saying he needed to speak with her.

As soon as they entered the office, he shut the door and kissed her. She pushed him away and made it halfway out the door when he caught her arm and yanked her back into the room so hard she tripped and went flying forward.

The last thing she remembered was her head slamming into his desk.

Emerging from the darkened office hours later, she noticed she was wearing the major’s green running shorts. She padded barefoot down a hallway to her office, where she found herself locked out. Two Marine guards found her outside the door, slumped on the floor, crying and shaking. She was certain she’d been raped.

“Call an ambulance,” she kept telling them, a plea she repeated to a captain and a colonel who arrived later.

Although the major who attacked her was discovered asleep in his office, naked from the waist down, no one heeded her requests for medical help and a forensic exam.

Instead, the colonel warned that if she went to a hospital, she would be prohibited from making a sworn accusation of rape because she’d been drinking. She would be charged with public intoxication and conduct unbecoming an officer, he told her.

“Dust yourself off. You’re tough. You’re from Colorado,” he said. “Whatever happened, it’s because boys and girls and alcohol don’t mix.”

That was her introduction to a military criminal justice system that frequently grants impunity to offenders and punishes victims, the outcome of a fiercely guarded power of commanders who wield broad discretion over the handling of sex crimes in their ranks, according to a San Antonio Express-News (http://bit.ly/15gWL9e) investigation.

The newspaper spent seven months examining how the military treats sexual assault reports, interviewing dozens of victims, advocates and experts and reviewing thousands of pages of military documents.

From the accounts of sexual-assault survivors in every branch of the military, a stark panorama emerges: Many victims were drugged or forced to drink and were raped, attacked as they slept, beaten unconscious and coerced into sex by their superiors. They were strongly discouraged from disclosing the crimes, or forced to report assaults to commanders who are closely connected to the accused.

Victims confront a system in which the investigators charged with pursuing their cases treat them with suspicion, rape kits are lost, guilty confessions are disregarded and jury verdicts can be vacated with the stroke of a commander’s pen.

Few suspects face criminal punishment. Of 3,374 reports of sexual assault last year involving 2,900 accused offenders, only 302 went to courts-martial and 238 were convicted, the Defense Department says.

Meanwhile, 286 offenders received nonjudicial or administrative punishment or discharges, allowing them to dodge a criminal mark on their record. In 70 cases, suspects slated for possible courts-martial were allowed to quit their jobs to avoid charges.

Prison sentences are rare. Only 177 perpetrators were sentenced to confinement. But the most jarring statistic: about half of all convicted sex offenders were not automatically expelled from the armed services.

The military had only recommended discharge for convicted offenders, but lawmakers cracked down this year and made expulsions mandatory.

While the lack of punishment for offenders is pervasive, many victims face reprisals from their superiors and are discharged with questionably diagnosed mental disorders.

For Helmer, the immediate response from her chain of command foretold the mishandling of her case.

She would face pressure at every turn to drop the allegations. Before it was all over, investigators responsible for pursuing her claim would doubt her credibility because she’d been drinking. And while the man accused of her rape would evade criminal punishment, she would become the target of an investigation by her superiors.

She watched her once-promising career end in ruins.

Naval Criminal Investigative Services ultimately told her the case could not go forward because she was unconscious and could not describe the assault.

“I said isn’t that the definition of rape? When someone violates you without your consent?” she said.

On the night she reported that she’d been raped, the colonel at Marine Barracks Washington refused to grant her medical help until she argued that her head injury demanded immediate attention. He agreed to let her go, but only after arranging for her to see a doctor he knew at National Naval Medical Center in Bethesda, Md.

“Don’t say anything else and come straight back,” he told her.

His instructions made the hair on the back of her neck stand up. She was put into a car with a captain who was supposed to drive her there. But she insisted he take her to a different hospital at Andrews AFB, where no one connected to the colonel would be awaiting her arrival.

She had a growing suspicion that the Marines she’d been trained to trust with her life did not have her back, and the Marine code of loyalty that drew her into service — Semper Fi, always faithful — did not apply to her, at least not if she spoke out as a victim of rape.

The attack in the major’s office was a betrayal by a superior she had trusted. But she eventually would regard the response from her chain of command and the military justice system as the biggest betrayal of all.

Flaws in the military justice system endure even after more than 20 years of infamous sex scandals and impassioned pleas for reform.

Against that backdrop last year came explosive details of young recruits who were lured into supply closets and empty dormitories, and sexually assaulted by their basic training instructors at Joint Base San Antonio-Lackland. So far, the Air Force has identified 33 instructors suspected of illicit conduct with 63 trainees.

Lackland has become the military’s biggest sexual-abuse scandal in the past decade, prompting congressional hearings in January and March and galvanizing support among lawmakers to remove oversight of sexual-assault cases from the chain of command.

New disclosures of wrongdoing are piling up. Just two weeks ago, Lt. Col. Jeffrey Krusinski, director of the Air Force Sexual Assault Prevention and Response Office, was charged with sexual battery after a woman accused him of groping her breasts and buttocks in a parking lot. And last week, the Army said it was investigating the coordinator of Fort Hood’s sex-assault-prevention program for abusive sexual contact and pandering.

In another case, an Air Force general’s decision to throw out a jury conviction of aggravated sexual assault ignited an uproar on Capitol Hill. Lt. Col. James Wilkerson, an F-16 pilot at Aviano Air Base in Italy, was sentenced in November by a jury of officers to dismissal and a year in jail for sexually assaulting a party guest as she slept in a spare bedroom of his house.

But in February, Lt. Gen. Craig Franklin, Wilkerson’s former commander, concluded the evidence was insufficient. Against the recommendation of his staff attorney, Franklin overturned the conviction, vacated the jury’s sentence and reinstated Wilkerson to full duty. He was reassigned to Davis-Monthan AFB in Tucson, Ariz., as chief of flight safety.

The case underscores the unchecked legal power of commanders. Although they typically have no background or training in the law and may not be impartial arbiters, senior officers like Franklin who are endowed with “convening authority” determine which cases go to trial, and they have the ability to overturn verdicts and vacate sentences before cases enter the appeals process.

Commanders are not required to follow legal advice on cases and they are allowed to weigh other criteria such as what they deem to be best for the good of the unit. According to military law, commanders can dismiss verdicts for any reason, or no reason at all.

Air Force officials said only five verdicts have been overturned in sexual-assault cases in the past five years.

In response to the case, Defense Secretary Chuck Hagel in April proposed that commanders be stripped of their ability to toss out trial convictions. Advocates contend the change doesn’t go far enough because the system still permits commanders to steer cases away from trial and reduce sentences.

However, Hagel and military brass oppose efforts to remove authority over sex crimes from commanders. At the Senate hearing in March, top military attorneys argued that sexual-assault cases must remain within the chain of command, and nothing less than the military’s ability to wage battle is at stake.

Evidence gathered by the Pentagon shows cases like the one in Aviano undercut the confidence of victims in the military justice system. The Defense Department estimates the vast majority of victims — about 89 percent — do not report sex crimes.

One of the main reasons: they view it as futile. Half of all female victims in an anonymous Defense Department survey released this month said they didn’t disclose sexual misconduct because they thought nothing would be done, and 43 percent remained silent because they thought they would not be believed. Testimony from basic training recruits at Lackland exposed how the vast imbalance of power between the ranks and the military’s rigid emphasis on submission to authority aggravate the problem. Not one victim at Lackland came forward, and some initially lied to investigators. Several testified that as their instructors sexually assaulted them resistance seemed impossible.

Others remain quiet because they’ve seen how victims are treated, ostracized by their units and punished by their chain of command. Reporting sexual misconduct widely is viewed as a career killer.

Many victims face explicit pressure from superiors to remain silent. Defense Department studies show victims in investigations tend to be younger (nearly 70 percent are under age 25) and lower-ranking. Thirty-eight percent of servicewomen in a 2012 survey indicated their assailant held a higher rank. One in four victims said the offender was in their chain of command.

Elle Helmer met the victim advocate assigned to her case at Malcolm Grow Hospital at Andrews AFB. Helmer had spent the previous five hours at the hospital, where a doctor who conducted her forensic exam noted she was “frightened and shaking” as the procedure started at 4:25 a.m.

The victim advocate arrived with instructions to drive Helmer back to the Marine Barracks. The colonel and executive officer wanted a word with her.

Helmer was confused. She thought the advocate was there to take her to Naval Criminal Investigative Services, which had jurisdiction over crimes at the barracks. Helmer was adamant that she wanted to make a statement at NCIS. The advocate warned against it.

“These cases never go anywhere,” she told Helmer, who was galled.

“And she’s the sexual response coordinator!” Helmer now says. “It felt like walking backward in time.”

The NCIS investigation lasted three days. Investigators closed Helmer’s case on the grounds she could not recall any sexual assault.

“Her statements did not constitute an allegation of criminal activity,” the NCIS report stated.

Frustrated by inaction and subjected to increasing antagonism from her superiors, she told her command that she was speaking to a reporter in Washington about her case. Although nothing was published, she was fired from her job and charged with conduct unbecoming an officer and fraternization.

She was dismissed from the Marines for unacceptable conduct in January 2007 with a “general under honorable conditions” discharge.

While she waited for her final dismissal papers, military authorities told her the rape kit had been lost.

Ultimately, the major faced no criminal or administrative punishment. He was allowed to remain in the Marines and later received a promotion.

Staff Writer Sig Christenson contributed to this report.