Carolyn Lerner, left, the new head of the Office of Special Counsel, during a senior staff meeting in her office on Dec. 6. (Bill O'Leary/WASHINGTON POST)

Carolyn Lerner had the Air Force’s top four-star general boxed in.

Gen. Norton Schwartz was reeling from revelations that the Dover Air Force Base mortuary had lost and sawed off body parts and mishandled other remains of America’s war dead. In the glare of television cameras, the Air Force chief of staff was forced to issue mea culpas for the scandal in November.

Lerner, the newly installed federal lawyer whose tiny office uncovered the gruesome findings, was ready for a fight.

Lerner accused the Air Force of deflecting blame — and a mortuary official of lying and obstructing the probe by firing one of the workers who blew the whistle. When Schwartz declared that Lerner’s Office of Special Counsel had prevented the military from notifying the families of the dead service members for more than a year, she dressed him down to the news media.

The claim was “patently false,” Lerner charged. It was Schwartz who resisted. The Air Force, her deputy said, showed “as much, if not more, reverence for its image as it has for the families of the fallen.”

Just six months on the job, President Obama’s fact-finder for federal wrong­doing had America’s military in her crosshairs.

Since she took over the obscure investigative unit that reviews disclosures of government wrongdoing — and advocates for employees who are punished for reporting it — the employment and civil rights lawyer, 46, has shown a willingness to shake things up.

In several high-profile cases, Lerner has gone to the mat and tried to expand the boundaries of the law’s protections for whistleblowers. She has lifted long-sagging morale at an agency that, instead of behaving as an independent watchdog, has treaded water for much of its existence.

Lerner’s staff is tackling neglected cases, in contrast to her predecessor, whose office had thrown many out, and claims have shot up since she arrived, Lerner says. She has challenged judgments by the panel that decides civil service disputes. And she has called for wholesale changes to the law prohibiting politicking by public employees so local and state workers can run for office, even if their jobs are tied to federal funding.

The bar is still high for Lerner’s office to pursue a case, but if the office thinks a case has merit, the federal agency in question must investigate within 60 days, a mandate that in the past routinely stretched to three times that long. Managers are being told they need to step it up.

In a WikiLeaks era, the special counsel is a throwback to painstaking truth-seeking, the nemesis of the indiscriminate document dump.

“There’s this new air in the room with Carolyn in that seat,” says Danielle Brian, executive director of the watchdog group Project on Government Oversight.

“We’ve had people in that job who were actually hostile to the mission of the agency. She’s embraced the mission.”

With an $18 million budget and 100 lawyers, the unit is a small dot on the federal canvas. Lerner, who left a partnership in private practice, calls it the “best-kept secret in the federal government.”

“I feel like it’s a very important agency with unlimited potential,” she says, spelling out her pledge to spending-weary lawmakers on Capitol Hill: She’ll save the government money, uncovering taxpayer rip-offs, waste and cost overruns.

“We get a lot of bang for the buck.”

A voice for others

Lerner had never been a whistle­blower or represented one before taking the five-year appointment, but she arrived with a reputation for fairness, and the Senate approved her nomination unanimously. Growing up in Detroit in the civil rights era — and with a grandfather who was jailed in Czarist Russia for criticizing the government — she learned that “I needed to stand up for those who couldn’t protect themselves,” she says.

Just don’t call her a flamethrower.

When her office revealed the findings at Dover, the media gantlet made her nervous. In 20 years in private practice, she had been on television once. She hates being the focus of attention.

Lerner, who lives in Chevy Chase and is on the board of a nonprofit group that advocates for workers with family responsibilities, is married to a lawyer and has two teenagers. She actively promotes telework and flex time for her staff — and dreams of a puppy she can bring to the office. (In her short spare time, she’s a matchmaker, boasting that she has put two married couples together.)

She’s also gracious and deferential, hesitating to opine on a subject unless she knows exactly what she’s talking about (“Let me refresh myself on the facts on that”).

Her supporters insist that her placid appearance masks a tenacious approach to her job.

“She’s a pit bull,” says Tom Devine, legal director of the Government Accountability Project, which defends whistleblowers. “Most effective advocates go out of their way to keep their personalities out of it.”

Lerner prefers the mediation room to the courtroom.

“Virtually every case, if you can get people to sit down and talk, can be resolved,” she says. Workplace disputes can be messy. Sometimes an employee who feels wronged just wants an apology, or the parties can agree on a change that would improve his morale — even if a court would not convict his employer.

“A lot of times, we would shake our head at the creativity,” said Stephen Chertkof, one of Lerner’s former law partners. “Through force of persuasion, she would resolve a huge percentage of cases.”

Changing perceptions

Whistleblowers come in many sizes, shapes and mental states. They’re either embraced as heroes or maligned as snitches, the tendency of many managers.

Every president since the special counsel’s office was created under Jimmy Carter has told whistleblowers they have a friend in the White House. But it hasn’t always worked out that way.

The agency has been largely irrelevant, whistleblower advocates say — languishing under Carter, gutted under Ronald Reagan and embroiled in scandal under George W. Bush, whose appointee, Scott Bloch, purged the staff of lawyers who disagreed with him and announced that he would not follow up on cases of discrimination based on sexual orientation. Bloch pleaded guilty last summer to scrubbing his computer while under investigation for retaliating against his staff.

But a probe he launched before resigning in 2007 is one that has dogged Lerner as she tries to move her office forward: an investigation of White House political operations headed by Bush chief strategist Karl Rove.

The investigation continued under a caretaker director, who 11 months ago issued a 118-page report describing frequent, politically motivated travel by seven Bush Cabinet secretaries and other top appointees in the 2006 election cycle. The officials claimed, wrongly, they were acting on official business, the report said.

It immediately riled Rep. Darrell Issa (R-Calif.), whose powerful House committee oversees operations. Issa has relentlessly investigated the investigation, questioning its accuracy and motivation. Lerner’s staff has turned over 25,000 pages of e-mails, memos and other documents that took her staff thousands of hours to unearth.

Issa, in a statement, said he has “seen some early good efforts” under Lerner’s leadership. But he expressed “substantial concern that the agency’s good-government mission is being tainted by improper political agendas.”

In response, said Lerner, “a lot of concerns were expressed about the agency under the previous special counsel. I have to live with that. I hope that over time the perception will change.”

So far, even some targets of whistleblowers say grudgingly that Lerner’s office is evenhanded. “When somebody’s accused of whistleblower reprisal, my sense is they’re being fair and reasonable with them,” said Bill Bransford, general counsel for the Senior Executive Service Association, which represents the government managers who often are accused of retaliating against whistleblowers.

Soon after she started, Lerner reassigned staff members to review a backlog of cases against whistleblowers — veterans hospital staff members reporting poor lab procedures, air traffic controllers claiming flight-pattern dangers — who were facing reprisals.

A Defense Department auditor demoted for blowing the whistle on her bosses about multibillion-dollar contracts being rubber-stamped to cut costs was exonerated. In November, the office got the panel that decides civil service law violations to reinstate the security clearance of a Marine Corps veteran punished for blaming top military officials for failing to speed the shipment of lifesaving vehicles to Iraq.

They were not as lucky with a scientist working for the Food and Drug Administration whose team found safety flaws with a mammography device to detect cancer and took them public.

The man was fired after poor evaluations, but the law exempts public health workers from whistle­blower protections — an exemption Lerner calls “ridiculous.”

“If we don’t have a safe and secure channel in place, they have to go outside the system and use a source like WikiLeaks,” Lerner says.

As for the Dover scandal, Defense Secretary Leon E. Panetta was forced to retreat from his out-of-the-gate praise for the Air Force’s “thorough” probe and what he called “appropriate” discipline. He ordered top brass to reconsider whether tougher punishment against mortuary officials is warranted.

Meanwhile, Lerner is fighting for the mortuary workers who blew the whistle and were demoted.