SAN DIEGO — As the Pentagon and the military services grapple with what appears to be a skyrocketing number of sex crimes within the ranks, the Navy has quietly been working on an extensive program it says has reduced the most serious sexual assaults by more than 60 percent at its largest training base — a decrease that has held for more than two years.

Now, the Navy is taking the lessons learned from that program and implementing the applicable parts of it across the fleet.

At Naval Base San Diego, that means specialized mandatory training and small-group discussions; reaching out to police, local colleges, hotel and bar associations and the local gay and lesbian community; new rules on alcohol sales; and nightly patrols of the areas around the barracks.

Patrols for trouble spots

Chief Petty Officer David Auxier went on the first such patrol at the San Diego base in February, when huge, rowdy parties in rooms and common areas were commonplace. He’s been on more than a dozen since, and things have “calmed down quite a bit,” he said.

One recent weeknight at around 9:30, Auxier and Petty Officer 1st Class Charles Dowding walked into a park near several barracks buildings, where small groups of sailors sat quietly in the dark, smoking cigarettes and sipping beer.

“You’ve got 30 more minutes,” Auxier told the sailors, many of whom had several empty bottles lined up on the cement picnic tables.

Auxier and Dowding didn’t hassle them, though they would go back later to make sure everyone had cleared out. From the park, they walked to a fence separating the base from the civilian world, and glanced into dark spots near a parking lot, to make sure no one was hiding or hurt.

Outside the fence, neon signs flashed “cocktails and dancing” and “adult emporium.”

Next, Auxier and Dowding walked to the bowling alley. Just one man was bowling, but the bar area was nearly full — another potential trouble spot. One man held up his beer to greet Auxier; most patrons seemed unbothered by the patrols.

The point of the patrols isn’t to stamp out fun or stop all drinking, said base Command Master Chief Scott Mathis. Instead, the senior enlisted leaders simply make sure that people are acting appropriately and following the rules. They also can offer help, advice or just a listening ear.

If they see someone standing by himself in the dark, they ask if they are all right. If they see a loud, drunken room party that consists of one woman and nine men, they make sure the woman is OK and send everyone home. If someone looks underage, they ask for an ID. And if their peaceful attempts to defuse a situation turn violent, or if they see criminal activity, they call security.

While the program was designed with an eye at preventing sexual assaults, Mathis said that since the patrols began, the base has seen a marked decrease in other crimes and misbehavior as well, such as DUIs.

That appears to be a trend Navy wide: There were 52 percent fewer alcohol-related incidents in May, June, July and August of 2013 than in the same time period of 2012, despite the fact that some of the alcohol-related policies and programs didn’t begin until mid-summer.

When the sailors see the chiefs walking up, in uniform, “It’s like, ‘Uh oh, time to act right,’” Auxier said.

Facing pressure to combat drug use and sexual assault at the Air Force Academy, the Air Force has created a secret system of cadet informants to hunt for misconduct among students.

Cadets who attend the publicly-funded academy near Colorado Springs must pledge never to lie. But the program pushes some to do just that: Informants are told to deceive classmates, professors and commanders while snapping photos, wearing recording devices and filing secret reports.

For one former academy student, becoming a covert government operative meant not only betraying the values he vowed to uphold, it meant being thrown out of the academy as punishment for doing the things the Air Force secretly told him to do.

Eric Thomas, 24, was a confidential informant for the Office of Special Investigations, or OSI — a law enforcement branch of the Air Force. OSI ordered Thomas to infiltrate academy cliques, wearing recorders, setting up drug buys, tailing suspected rapists and feeding information back to OSI. In pursuit of cases, he was regularly directed by agents to break academy rules.

“It was exciting. And it was effective,” said Thomas, a soccer and football player who received no compensation for his informant work. “We got 15 convictions of drugs, two convictions of sexual assault. We were making a difference. It was motivating, especially with the sexual assaults. You could see the victims have a sense of peace.”

Through it all, he thought OSI would have his back. But when an operation went wrong, he said, his handlers cut communication and disavowed knowledge of his actions, and watched as he was kicked out of the academy.

“It was like a spy movie,” said Thomas, who was expelled in April, a month before graduation. “I worked on dozens of cases, did a lot of good, and when it all hit the fan, they didn’t know me anymore.”

The Air Force’s top commander and key members of the academy’s civilian oversight board claim they have no knowledge of the OSI program. The Gazette confirmed the program, which has not been reported in the media through interviews with multiple informants, phone and text records, former OSI agents, court filings and documents obtained through the Freedom of Information Act.

When Xatavia Hughes, the granddaughter of a military man, went to serve in Iraq, she was prepared to prove herself to the male soldiers.

"My grandfather was tough and strong. That is how I was brought up: 'Don't let it get to you. Show them,'" the 28-year-old mother of two said.

And she did. It was only after she returned from a war zone to Chicago in December 2010 that Hughes began to feel tested.

A month after returning, Hughes found herself in an improbable spot: living in a dorm room at the Pacific Garden Mission, the sprawling homeless shelter on the city's West Side, shielding her two sons from addicts and criminals.

"Often when I was in shelter there was a bunch of veterans," Hughes said of her six months of homelessness. "When we get out, I thought we were supposed to be taken care of. And I was like, 'Wow, this is how our life is going to be?' I never felt that I would do so much good and then have to be pushed aside."

Hughes was like so many women over the past decade who stepped up to serve as the country launched two wars. They saw it as a way to get ahead in life and forge a different future.

Women have become the fastest growing segment of the veteran population, a trend that is expected to continue. Their return has posed several new issues for the Department of Veterans Affairs. Many are single moms. They have been adversely affected by the scandal of military sexual trauma that affects one in five women who serve. They report higher rates of mental health illnesses and homelessness. Many don't feel comfortable in the male-dominated VA.

And though they already served in dangerous, life-threatening positions, the recent decision to allow women to fight in combat zones means even more are likely to return with complex and severe injuries that need attention.

Local VA hospitals have improved care and increased services for women vets, even down to their design and architectural elements. A new housing complex for veterans with families is scheduled to open next summer, offering some relief. The VA launched a hotline just for female vets in the spring.

And in the latest recognition of the need for services, a long-standing community mental health organization, Thresholds, this year expanded its existing veteran services, assigning more case workers to connect with female vets struggling on Chicago's streets.