This photo provided by Franz Gayl, a retired Major, shows Gayl in 2006 as a civilian science adviser in Iraq. Franz Gayl/AP Photo
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A Navy review board has overturned a Marine Corps decision to strip one of its senior science advisors of his security clearances, intervening directly in a case that attracted attention among lawmakers on Capitol Hill and among advocates of enhanced legal protection for military whistleblowers.

Franz Gayl, who complained publicly in 2007 that the Corps had squashed an urgent request from U.S. soldiers in Iraq for heavily armored vehicles, was stripped of his clearances last year and suspended indefinitely with pay. The Corps acted after alleging that he improperly placed a thumb drive in his restricted office computer.

Gayl promptly accused his superiors of retaliating for his whistleblowing, and sought legal protection. But the Corps twice sought to end his pay, most recently in September. The last attempt was thwarted by the Office of Special Counsel, an independent agency, which asserted in a legal filing last month that Gayl “is a public whistleblower who has put his career at risk out of concern for the safety of service members in combat.”

The Navy board, ordering an abrupt turnaround in his predicament, said in a statement to Gayl on Nov. 7 that he was again eligible for needed clearances, even as it chastised him for “disregard for direction from your supervisor” and for failing to follow security procedures. Marine Brigadier Gen. Michael A. Rocco, who directs the Corps’ strategy and plans division where Gayl worked, responded with a message to Gayl that “I have decided to cancel the proposed indefinite suspension.”

Underpinning Gayl’s longrunning dispute with the Corps was its resistance to a wrenching policy shift at the height of the Iraq conflict away from the longstanding development of two new light troop and amphibious carriers to the quick production of a heavy vehicle, known as the MRAP, which officers and soldiers in Iraq said they needed to protect them from roadside bombs.

The shift was ordered in 2007 by Defense Secretary Robert Gates, who made MRAPs the Pentagon’s top procurement priority partly because of news reports recounting Gayl’s complaints about Marine Corps foot-dragging. To the chagrin of some Corps leaders, one of the lighter carriers was eventually cancelled because of its high costs and other problems.

In meetings with lawmakers that year, Gayl accused the Corps leadership of institutional inertia and said its commanders were too wedded to programs that were already funded; he further charged that their failure to monitor and respond to an urgent request from the battlefield had caused needless deaths. He argued that his remarks were protected by civil service whistleblowing protections.

Then-Sen. Christopher Bond (R-Miss.) and then-Sen. Joseph Biden (D-Del.) wrote a joint letter warning the Corps not to punish Gayl; nonprofit groups such as the Project On Government Oversight organized a petition offering support. But after the Corps suspended Gayl for allegedly disregarding regulations and what it said was “a pattern of poor judgment and intentional misconduct,” Biden decided he could not intervene from the Vice President’s office, according to one of his aides.

After the special counsel’s office demanded a 45-day stay of the Corps’ decision to cut off Gayl’s pay this year, the Merit Systems Protection Board — an independent, quasi-judicial agency that polices civil service rules — issued the first official rebuke to the Marines. It concluded on Oct. 13 that “there are reasonable grounds on which to believe that Mr. Gayl’s indefinite suspension is a result of his protected activity and is therefore prohibited.”

The final decision, by a group formally called the Navy Central Adjudication Facility, came four weeks later. “I am very encouraged that the Pentagon appears to have finally come to the realization that Mr. Gayl is not the enemy, and that our military will be much safer if whistleblowers are valued and not exiled,” said Jonathan Cantu, his attorney at the nonprofit Government Accountability Project in Washington.

A spokesman for the Marines, Maj. Stewart Upton, said “personnel matters involving federal employees are subject to privacy laws and regulations. The Marine Corps takes very seriously the proper handling and resolution of any employee issues, and as in any other case we are taking the appropriate actions.”

Gayl, in a statement released Wednesday morning by the Project, said that “I am as committed as ever to return to the Marine Corps to work hard in support of all Marines.”

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R. Jeffrey Smith worked for 25 years in a series of key reporting and editorial roles at The Washington...