It seemed like a simple David and Goliath story.

Three military whistleblowers took on a powerful and vindictive admiral, accusing him of retaliating against them after he thought they were daring to speak up. And with the help of a few brave senators, the whistleblowers ended the career of the Navy’s top SEAL before he could launch another witch hunt.

“Admiral [Brian] Losey appeared to be a serial ‘retaliator.’ The evidence was overwhelming. He allegedly broke the law,” said Sen. Chuck Grassley (R-IA) in April.

But an investigation by The Daily Beast into the case of Rear Admiral Losey—including dozens of interviews and a review of hundreds of pages of previously undisclosed documents—reveals a far more complicated narrative.

One of the whistleblowers, it turns out, had been previously reprimanded for “criminal” conduct that impeded a military investigation. Another was implicated in a payroll scandal that cost the military tens of thousands of dollars.

And while the documents and interviews show the ultra-direct, constantly demanding Losey to be no one’s idea of an ideal boss, top defense officials call the seemingly damning Pentagon inspector general’s report that has ended his 33-year tenure “deeply flawed” and filled with “cherry-picked evidence.”

Today, there’s an after-the-fact counteroffensive under way to repair Losey’s reputation. His former boss, retired Navy SEAL Admiral William McRaven, recently took the rare step of speaking up in public. He called Losey’s ouster a “miscarriage of justice” that is part of “a disturbing trend in how politicians abuse and denigrate military leadership, particularly the officer corps, to advance their political agendas.”

That push has come too late to save the embattled admiral’s career. Losey—who once led the Naval Special Warfare Development Group, aka SEAL Team 6, and now leads its parent organization, the Naval Special Warfare Command—has filed his retirement papers, even though Secretary of the Navy Ray Mabus said there was “insufficient evidence” to conclude the one-star admiral retaliated against the three employees, according to an Oct. 16, 2015, letter seen by The Daily Beast.

***

The story starts five years ago, in Stuttgart, Germany, home to the U.S. military’s Special Operations Command Africa. Once a sleepy outpost, Stuttgart became a frantic military operations center after 2011’s Arab Spring set Africa on fire.

The command had been responsible for little more than running training exercises and building a Rolodex of African military contacts. But as conflict spread across the region, it quickly began assisting missions combating Libyan dictator Muammar Gaddafi in Libya, al Qaeda-linked Shabab in Somalia, Boko Haram in Nigeria, and the Lord’s Resistance Army in Central Africa, to name a few. The command’s staff doubled, and its pace of operations did all that and more. The admiral and his staff complained that three men who would later become whistleblowers weren’t keeping up.

When Losey got to the command in July 2011, he asked the two questions that he believed were key to running a military headquarters: Where are my people? Are we recognizing their service correctly? At previous commands, he’d relied on tools called “trackers”—spreadsheets to show daily who was where in the region, when his staff at headquarters was due to arrive or depart post, and who was due for the awards that were key to employee advancement.

For months, he asked two members of his staff—an Air Force officer who handled personnel matters, and his civilian chief of staff, Fredrick D. Jones—to build those tools so he could track personnel at his headquarters and the deployments of some 500 people across Africa.

Time and again, the spreadsheet-like tools weren’t delivered, according to letters of counseling to the two employees.

“I asked for a personnel tracker (in early summer) and still don’t have one,” Losey wrote in a performance review of chief of staff Jones that was part of the admiral’s defense of his case, sent to then-Special Operations Command’s Chief McRaven.

“My contact time with you amounts to 10 minutes a day on average,” Losey complained to Jones.

“Emails I send to you are seldom acknowledged, and the status of any action I request is not provided unless I ask for it,” he continued. “I have sent you 490 emails… You have sent me 76.”

Losey eventually moved Jones into another job in late fall 2011. The civilian chief of staff was demoted to “director of staff.” Jones had the same grade and pay but now answered to a military officer who Losey felt was more up to date with current combat operations, and more willing to put in the 24/7 pace.

Jones griped that Losey only gave him two weeks to improve after that letter of counseling before shifting him to the lesser post.

“I understood that I needed to make changes in order to better meet his expectations,” Jones wrote in an email to The Daily Beast. “However, only 15 days after this discussion took place, [Rear Admiral] Losey removed me as his Chief of Staff, which from my perspective was hardly enough time to implement all the changes he expected.”

The Air Force officer, who The Daily Beast is not naming because he was not linked to any misconduct, was first stripped of his duties, then moved to an equal job at European Command in the same city. He was told nothing would go in his record. He later told investigators he feared that future command boards considering his promotion would look askance at the mid-job move, and he blamed the action on Losey’s suspicion he’d made anonymous complaints rather than because of poor performance.

Just a month or so before those reassignments, someone had contacted the Defense Department’s inspector general to report that Losey tried to buy a plane ticket for his daughter on the government’s dime.

The allegation was quickly investigated and dismissed as spurious, and the case closed in just four days. But the Air Force officer later told investigators that Losey wasn’t satisfied with the clean bill of professional health. The officer said the anonymous tip left the admiral angry, and he shared his frustration and suspicions with his immediate staff.

The new chief of staff who replaced Jones in November 2011 was Army Col. Michael Franck. He’d been working at the command under the previous commander, so he’d seen how the mission had doubled in the two years since he arrived in 2009, going from 250 troops deployed across the region to 500. He saw change so rapid, some couldn’t keep up.

“There was just a lot more work to do,” Franck said in an interview with The Daily Beast.

The three men who would eventually bring Losey down had a very different point of view. They saw every complaint about their performance through the lens of their commander’s outrage over the original travel complaint. And, eventually, the Defense Department inspector general seemed to take the same point of view.

Clearly, there was tension in the air. On Nov. 17, the inspector general of U.S. Africa Command received an anonymous tip, this time about the “toxic” environment in Losey’s shop.

Losey’s response, according to a later inspector general’s report: “If you continue to undermine my authority as a commander, I’m going to bury each one of them. I’m going to come after them, and I’m going to [make] it very unpleasant.”

Losey’s lawyer denies the outburst ever happened, and the inspector general report concedes it was a one-on-one conversation with no other witnesses.

But documents including performance reports, email exchanges, and legal records of investigations show a frustrated commander accustomed to working at high speed with a willing staff dealing instead with constant questioning of his requests and commands.

“It chafed them,” Franck said of a small group that included Jones. “They were being asked to work harder than before and they didn’t like it. They started rebelling.”

***

What Franck hadn’t expected when he took the chief of staff post was the budgetary time bomb that landed on his desk shortly after he took over. The staff had racked up hundreds of hours of outstanding “comp” time or overtime that would have to be paid for, and the command didn’t have a budget for it.

Former chief of staff Jones had never told anyone this was looming, and upon systematically investigating the payroll of the entire command going back to the pre-Losey era, Franck found that Jones and a small group of his closest work associates had racked up the most time.

Losey issued new orders regarding overtime, and Franck eventually asked for a formal investigation the following summer, centering on those with the most to gain from the scheme.

The AR 15-6, as it’s known, showed that Jones had been using subordinates to approve his extra hours plus other irregularities long before Losey arrived and in contravention of a 2009 personnel policy in force. It amounted to a cabal of employees who worked together for years at the headquarters and were signing off on each other’s overtime, worth thousands of dollars in extra pay every month.

The investigation found Jones had “subordinates certify his time and attendance, premium pay, and leave records on at least 55 occasions”—some of those occasions, after Losey had issued the new orders.

Jones insists later investigations by the parent Africa Command cleared him of any wrongdoing, referring to documents The Daily Beast was not able to access.

One of the people who signed off on Jones’s overtime was the command’s executive officer, Robert Gwinner, another senior civilian staffer. Neither Jones nor Gwinner were punished for the pay infractions, but they were warned not to do it again. (Daily Beast attempts to contact Gwinner through Africa Command and his LinkedIn profile were unsuccessful.)

It wasn’t Gwinner’s first tangle with the military brass.

In a March 20, 2004, letter shared with The Daily Beast, then-Maj. Gen. Ray Odierno formally reprimanded Gwinner, who was in charge of troops in the 3rd Brigade combat team of the 4th Infantry Division, for “wrongfully impeding a criminal investigation division investigation into the drowning death of an Iraqi citizen.” Odierno, who later became Army chief of staff, said Gwinner instructed soldiers “to deny that two civilians were pushed into the Tigris River which was totally false. Your conduct was wrongful, criminal and will not be tolerated.”

Gwinner claims he got a poor mark on his 2011 employee review, however, because he was suspected of making one of the whistleblower complaints. Inspector general investigators agreed, as Gwinner was downgraded by Losey from the highest mark to the “Success All or Excellence,” the second-highest mark an employee can be given. The inspector general berated Losey for failing to give Gwinner an “improvement plan,” but defense officials countered that the rating was too high to trigger that, and Navy officials said the decline in review was merited because of documented lackluster performance.

One email exchange in Losey’s letter to McRaven provides a snapshot of a clash of cultures between retired Army officer Gwinner and the SEAL admiral. The surreal seven-email volley starts with Losey reminding Gwinner to remove the liquor on display in his office, as the admiral didn’t want troops coming in from African conflict zones to see a double standard, with alcohol forbidden overseas but permitted at the headquarters.

Instead of saluting smartly, saying, “Yes, sir,” and removing the alcohol, Gwinner writes back in the Sept. 24, 2012, email exchange complaining that if he has to remove alcohol from his office, others should be forced to do the same.

One of the responses read: “Sir, Just to clarify, your original request 15 month[s] ago was to remove the alcohol from open display; you further stated it was okay if I placed it in the cabinet under the printers, which I immediately complied… At this very moment, there is alcohol in your own command group in the refrigerator. V/R,Mr. Gwinner”

The anonymous report of a “toxic climate” triggered then-Africa Command chief Gen. Carter Ham to ask for an independent investigation of the headquarters. According to a report by now-retired Lt. Gen. Ray Palumbo, Losey’s leadership wasn’t toxic, but it was direct—admired by most, but uncomfortable for some that he anonymously interviewed.

“Rear Adm. Losey’s forceful and no-nonsense leadership style pushes the limits of tolerance for some employees who remain comfortable with the old culture,” Palumbo wrote in a report obtained by The Daily Beast. “Several of these employees… are either unwilling or unable to adapt to the new direction and tempo being set for the command.”

That strain plus the constant drumbeat of investigations into Losey created an “undercurrent of drama” that Palumbo said was distracting to all, but he said the command was performing well during a high-tempo, demanding period, and he concluded that “Losey is the right man for the job at this time.”

Africa Command Chief Ham, who’d commissioned the Palumbo report, counseled the younger officer on its findings.

“Brian was not a perfect leader,” Ham said in an interview. “He’s a hard driving, high standards person, and he is also very direct, and that can sometimes be off-putting.”

Ham told him to ease up.

“You’ve got to make some adjustments to your leadership style,” Ham remembered telling Losey.

“My sense is Brian took that to heart,” he said.

The Defense Department’s inspector general, however, had a very different point of view, finding him guilty of reprisal in three out of five cases.

***

When the inspector general’s report landed on the desk of Secretary of the Navy Ray Mabus last fall, it concluded Losey had, in fact, retaliated against employees. The IG said Losey lowered two employees’ annual performance evaluations and removed a third from his staff and reassigned him to a staff position at a higher headquarters, all because he suspected them of making those anonymous complaints in the fall of 2011. (Ironically, none of men were the original “whistleblowers.”)

Losey’s aide Franck was later investigated too, to see if his investigation of the pay issues was reprisal for whistleblowing, but he was cleared of wrongdoing by the Army. Another member of Losey’s staff, now-retired Air Force Col. Richard Samuels, denied retaliating against anyone but offered no further comment in a brief phone interview. The Air Force declined to take action against Samuels.

Whistleblower caucus founder Sen. Grassley mentioned a fourth outstanding investigation against another unnamed member of Losey’s staff in a statement regarding the case, but the Air Force spokesman’s officer could neither confirm nor deny the investigation, citing the privacy laws.

All of this left the secretary of the Navy, Mabus, will some heavy decisions to make about Losey’s future.

Before acting, Mabus assigned the Navy’s first woman four-star, Vice Chief of the Navy Admiral Michelle Howard, the task of judging the case and, if necessary, punishing Losey, who had been put in charge of all the Navy SEALs despite the investigation hanging over his head.

After reviewing both the inspector’s reports and evidence submitted by Losey, Howard found fault in all parties, senior officials said. In an Oct. 1, 2015, letter seen by The Daily Beast, she wrote that Losey had taken appropriate action regarding the three alleged whistleblowers, whom the records showed were poor performers.

But she also lectured Losey for expressing his frustration to his immediate staff over a whistleblower complaint filed within his first year of command that falsely accused him of billing the Navy for his daughter’s travel.

“You conveyed your frustration that a member of your command would take issue with your activities and contact the inspector general without addressing you first,” she wrote in the missive, which officials say was followed up by a lecture via video teleconference. “You created a perception in those who heard your comments that they were constrained in their reporting options.

“As a leader, you must be more mindful of the effect of your communications and how they can be perceived by others,” she concluded.

Howard considered verbal and written counseling enough to steer the experienced officer on the right path, especially as anonymous surveys of his troops both in Stuttgart and Coronado gave him high marks for “command climate,” proving to her that he’d learned from his time in Germany, senior officials said.

In his first public comment on the case, Losey said he took the lecture to heart.

“‎I appreciate the diligence and thoroughness the Navy exercised in reviewing and adjudicating this matter,” Losey wrote in an email to The Daily Beast. “And, I absorbed the counseling points provided by my superiors.”

Mabus endorsed his vice chief’s decision and told the Pentagon inspector general that there was “insufficient evidence” to conclude Losey retaliated against the three employees, according to an Oct. 16, 2015, letter seen by The Daily Beast.

The Pentagon Office of the Inspector General declined to comment.

But senators who have long championed the rights of whistleblowers saw a case of the top brass steamrolling their own investigators—all to benefit a powerful admiral. Sen. Ron Wyden (D-OR) placed a hold on the Navy’s nomination of Dr. Janine Davidson for a senior Navy post. The leaders of the Senate Armed Services Committee, Sen. John McCain (R-AZ) and Jack Reed (D-RI), also sent Mabus a letter saying they’d never have agreed to give Losey a second star by Senate vote back in 2011 if they’d known about the allegations.

That letter “sends a message to whistleblowers: Reprisal will not be tolerated. That’s a real morale booster for all whistleblowers suffering under the weight of reprisal,” said Sen. Grassley in a speech on the Senate floor in April. “Holding such a distinguished naval officer accountable was no easy task. To the contrary, it was as difficult as they get.”

Mabus eventually bowed to the lawmakers’ demands.

“The secretary of the Navy had to make a call,” according to a defense official briefed on Mabus’s decision-making process. “He put the organization ahead of the individual.”

Two defense officials said Losey has filed his retirement papers and has been handing over duties to his named replacement, Navy SEAL Rear Adm. Tim Szymanski.

Losey’s case has left a lasting bitterness at the Pentagon, where multiple senior officials were eager to share their take on what they see as justice gone wrong.

But Grassley said Losey “can only blame himself for what happened… That’s accountability’s harsh reality. He allegedly broke the law and must now pay the price.”

On the House floor Friday, retired SEAL officer-turned-Republican Congressman Ryan Zinke, rejected that. “He saw a problem and took action,” Zinke said of Losey. “An entrusted, entrenched bureaucracy was allowed to hide behind threats, hide behind whistleblower…rules that were intended to protect command and not to erode it.”

Losey does not believe he broke the law, but in his email to The Daily Beast, he indicated he’d accepted the Navy’s decision.

“I have accepted full accountability and responsibility for my actions,” he wrote.