WASHINGTON– A self-described “recovering budget geek” who spent four years as the Pentagon comptroller, Deputy Defense Secretary William J. Lynn III said what drives him as he crunches numbers and relentlessly scrutinizes Defense Department programs and systems is knowing their impact on front-line troops.

Lynn is Defense Secretary Robert M. Gates’ man behind the scenes who focuses on the department’s day-to-day operations. He’s been called the Pentagon’s “city manager” to Gates’ “mayor.” But the business-minded Lynn prefers to think of himself as a chief operating officer to Gates, the CEO.

“Secretary Gates is doing more of the external role, interacting with the White House, dealing with the conflicts,” Lynn explained during an interview earlier this month on the flight back to Washington after one of his relatively rare public appearances.

“I am more focused on the internal management of the Pentagon, the acquisition process, the public process, the personnel processes,” he said. “I’m responsible for ensuring the department’s smooth functioning – which technologies to use, which weapons to buy, which business operations to employ.

“So this is a classic inside-outside, CEO-COO kind of division of labor.”

Lynn appears happy to stay out of the limelight as he oversees a portfolio bulging with relatively unsexy – but highly consequential – Defense Department issues. He makes relatively infrequent public appearances, typically to talk with targeted audiences about specific initiatives on his plate.

He traveled to an aerospace and defense conference in New York earlier this month to bolster closer cooperation between the department and industry to support warfighters’ needs. Last month, he visited his alma mater, Cornell University Law School, largely to encourage government or military service.

Earlier that week, Lynn explained at a Defense Information Technology Acquisition Summit the importance of acquisition reform initiatives under way to make the system more responsive to warfighters’ needs, and the need to protect the department’s vast networks against the growing cyber threat.

Lynn sometimes gets to show his “softer” side during events that draw him closer to the base he strives to serve: servicemembers and their families. He recognized during an address early last month the need to do more for the military families who provide the backbone behind the force. And shortly after arriving at the Pentagon, he opened a family workshop touting the way beloved Sesame Street characters are helping military kids adjust to their parents’ redeployments.

But for the most part, Lynn remains nose-to-the-grindstone, keeping two major projects front and center on his ‘to-do” list: the fiscal 2011 defense budget request and the Quadrennial Defense Review, a massive 20-year look-ahead that leaves no rock unturned in the department. Both are actively in the works, scheduled to go to Congress early next year.

As he works these and myriad other issues, Lynn draws on every building block of experience on his extensive resume. He spent six years on Capitol Hill, as the late Sen. Ted Kennedy’s liaison to the Senate Armed Services Committee. Eight years with private industry, most of it as a senior vice president for Raytheon, gave him valuable insights he applies every day.

In addition, Lynn is no stranger to the Pentagon. He served as comptroller during the Clinton administration, and before that, directing the Pentagon’s program analysis and evaluation office. Those were the days of U.S. military missions in the Balkans and Haiti, smaller-scale operations that centered on peacekeeping.

Lynn returned to a very different Pentagon – one on a solid war footing, with sustained combat operations under way in two theaters. “That influences everything that you do in a very fundamental way,” he said.

Despite so many changes, Lynn cited a constant. “The talent and dedication of the military has not changed since I left,” he said.

He saw these traits in action in September, when he paid a quiet visit to Iraq and Afghanistan, accompanied by the Dallas Cowboys Cheerleaders, who garnered most of the headlines.

Lynn told a USO group after his return he felt inspired by the spirit of troops he chatted with as they pulled duty on a dusty base, worked on a flight line, relaxed in the mess hall and recovered in the hospital.

“Like generations before them, our soldiers, sailors, airmen, Coast Guardsmen and Marines are doing an extraordinary job,” he reported.

Lynn said he felt gratified knowing the role he’s helping to play – particularly through his budgeting and acquisition duties – to provide them the tools they need to succeed.

“We have to make sure that we provide the best technology we can bring to the fight, and in sufficient numbers to counter the threat,” he said. “Ultimately, what we do is all about defending our security, and enabling the men and women who are on the front lines to get what they need, when they need it.”

As the implementing force behind Gates’ defense acquisition reform effort, Lynn said, he understands the importance of cutting inefficiencies and cost overruns to better meet those needs. He’s taken on the challenge with his eyes wide open, recognizing that “repeated attempts at reform by smart, dedicated people” have failed to fix core problems, despite the benefit of more than 130 commissions and studies examining the acquisition process.

Calling this long track record “cautioning,” Lynn said he believes the stars are finally aligned for positive change. The president, Congress and Pentagon are all on the same sheet of music, he noted, committed to making the difficult and sometimes unpopular decisions that true reform requires.

“I think we come at it with an approach that there is no ‘silver-bullet’ solution,” he said. “You have to undertake a series of targeted steps.”

Lynn said he’ll gauge his effectiveness at deputy defense secretary largely on how well those steps lead to reform.

“If we succeed at a reform agenda that upgrades the acquisition process, makes the budget and resource allocation process more responsive, that would be a significant success,” he said.

And, Lynn said, he wants to posture the department to defend its networks and protect access to the cyberspace domain. He supports the stand-up of a new Cyber Command, under U.S. Strategic Command, and said he wants to be instrumental in filling in the doctrinal and legal foundation needed for it to fully succeed.

These aren’t easy issues, he concedes, but said he’s committed to help in working through the challenges. The trick, he said, is focus on the big picture and to not get bogged down in minutia.

“You have to keep your head above water a bit to focus on the major objectives,” he said. “You can get overrun by the day-to-day need to move things from the inbox to the outbox. You can’t ignore that, but you can’t get consumed by it, either.”

Challenges, it seems, are what attracted Lynn back to the Pentagon, and what keeps him motivated, day in and day out, as deputy secretary.

He told the Senate Armed Services Committee during his confirmation hearing in January he would approach the job with humility. “Serving as the chief management officer of an organization as large and diverse as the Department of Defense is a task that no one is truly qualified to perform,” he said.

But as one colleague, who asked not to be named, attested, few others could bring such a wealth and breadth of experience and capability to the job.

“He’s a wizard. He’s absolutely brilliant,” he said of Lynn. He cited Lynn’s Capitol Hill and comptroller experience, but also corporate smarts a department executive who’d risen through the ranks might not bring to the table.

“I watched him and his operation [at Raytheon], and how he did the bigger-picture strategic planning and thinking for the company, which was his job,” the colleague said. “What struck me most was his agility to go completely out of the box.”

It’s an ability Lynn draws on heavily in his position. “In my mind, the decision to bring him back as deputy secretary was brilliant,” the colleague said. “I was ecstatic when I saw that happen.”

Approaching his first-year anniversary on the job, Lynn said he’s still excited about the opportunity to make a difference.

“This is an excellent job,” he said. “There is always a new challenge, so there is never a lack for things to

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