By Mark Thompson / Washington Thursday, Nov. 13, 2008

Mullen speaks to Marines in Iraq . He needs to help his new boss shift forces to Afghanistan .

Mike Kemp / Getty

Next to a non-denominational prayer room up in the Pentagon's attic, the ways and means of Barack Obama's foreign policy are quietly taking shape. There, in a decidedly unglamorous and narrow office that was once a hallway, sits the Chairman's New Administration Transition Team (CNATT), where a dozen midlevel military officers have been working to prepare briefings for the next President on America 's two wars and other hot spots overseas.

There's an intense hum in this out-of-the-way place. Murmured conversations over secure phone lines mix with keyboard clicks. Officers from all four military services are reviewing war plans, threats to national security unknown to the rest of us, and enough PowerPoint briefings to choke a presidential campaign. The CNATT is by far the most important of all the secret teams around Washington now madly churning out to-do lists for the President-elect.

The Pentagon team has for months been tracking Obama's foreign policy and military statements . It has studied his advisers and their backgrounds. The CNATT hasn't generated a written report telling Obama what he should do or even offered options for Iraq , Afghanistan and elsewhere. Instead, it will listen to what Obama has in mind, and then detail for him the corresponding risks and benefits. Obama's transition team, says Admiral Mike Mullen, Chairman of the Joint Chiefs of Staff, "will be in here very quickly ... to start to come up to speed." Obama called Mullen two days after the election to say he's "looking forward" to working together.

As Mullen likes to point out, Washington has not been through a presidential transition in wartime since 1968. Now, almost 40 years after Vietnam , Obama is inheriting not just one war, but two. The importance Mullen places on getting the handoff right can be seen in the fact that he put the front office of the CNATT on the Pentagon's exclusive E-ring corridor, right next to "the tank," where the Joint Chiefs conduct secret strategy sessions on the wars.

Mullen's first challenge will be to help his new boss shift forces from Iraq to Afghanistan without jeopardizing the gains in Iraq . While U.S. commanders in Baghdad are leery of additional cuts, Mullen and his fellow Chiefs — along with Obama's team — are already contemplating them. "It's a huge balancing act," Mullen says.

Although the Pentagon team is focused on Iraq and Afghanistan , "We have to be careful we don't miss other bubbling crises because we're so wrapped up in the wars," a senior Defense official says. Mullen is concerned that — as Senator Joe Biden predicted during the campaign — enemies overseas may try to test the U.S. during the transition, or challenge the will of the new President after a contentious campaign. More likely is an early overseas incident that catches the Commander in Chief and his team off guard. The unraveling of Somalia in 1993 led to the deaths of 18 U.S. troops in Bill Clinton's first year in office. And President George W. Bush had been on the job a little over two months when a midair collision between a Chinese air-defense fighter and a U.S. Navy EP-3 surveillance plane resulted in 24 U.S. crew members hostage for 11 days. "History is replete with such tests over the past 40 to 50 years," Mullen says. "Given that, I want to be prepared in case we are."

On Wednesday, Obama aides said his Pentagon transition team would be headed by Michele Flournoy, president of the Center for a New American Security, and John White, chair of the John F. Kennedy School of Government's Middle East Initiative at Harvard University . Flournoy says transitions are vulnerable times because political appointees often aren't yet in place, leaving the military to run largely on autopilot. A senior Pentagon official during the Clinton Administration, Flournoy knows that from reviewing what went wrong in Somalia that led to the disaster known as "Black Hawk Down."

"You could see the slow-motion derailment of the train," Flournoy said, before being named to head the transition team. "There really wasn't anybody home to do the day-to-day oversight." The Obama camp has already provided names to the FBI in hopes of having a cadre of political appointees ready to assume command quickly.

Mullen, according to aides, sees three areas of potential trouble:

Pakistan : The country's new civilian government remains shaky, and its recent attacks on Islamic militants in its tribal areas bordering Afghanistan have angered much of the population. The stakes are enormous because Pakistan possesses the Muslim world's sole nuclear arsenal. Only by getting rid of the militant sanctuaries inside Pakistan , military officials believe, do the U.S. and its allies have any chance of prevailing in Afghanistan . Wiping out the safe havens while keeping Islamabad 's nuclear weapons secure will be a complex challenge.

Iran : Tehran 's dogged push to develop nuclear power — and, the West maintains, nuclear weapons — may come to a full boil in the next year. Some international experts say that Iran will soon be in a position to produce enough enriched uranium to build a bomb, a threshold that could force the hand of the new President, if not the government of Israel. Obama has declared that Iran will not be permitted to become a nuclear-armed state — a vow that could soon set the stage for a military confrontation if stepped-up diplomacy and sanctions continue to produce no change in Iran 's behavior.

Terror Inc.: Mullen's biggest concern continues to be another 9/11. He has told confidants he's haunted by the prospect of a strike on U.S. soil as the White House changes hands: "I am extremely concerned that the terrorists who still target us could come at us during this period of time."

Mullen has been careful to avoid being seen by Obama to be "shaping an agenda", says a Joint Staff officer working on the transition. "He wants to make sure we stay away from the political process and just provide the advantages and dis-advantages of a given policy." Colin Powell — who endorsed Obama and who has been through this drill, first as Joint Chiefs Chairman and later as Secretary of State — noted that for military officers, "the most important thing is to let the incoming team know that we are professionals. We have no politics: The King is dead. Long live the King."

The 62-year-old Mullen, one of the oldest officers in uniform, is well suited to the task. He was a freshly minted ensign right out of the Naval Academy 's class of 1968 when Lyndon Johnson bequeathed the conflict in Vietnam to Richard Nixon. At the time, Mullen was serving aboard a destroyer in Long Beach , Calif. He went on to command three ships, as well as a carrier battle group, before becoming Chief of Naval Operations in 2005. The first Navy man to lead the Joint Chiefs in 20 years, he got the military's top job after Defense Secretary Robert Gates declined to nominate Marine General Peter Pace for a second two-year term as Chairman. Many saw Pace as too closely linked to former Defense chief Donald Rumsfeld and his floundering Iraq policy, a burden Mullen doesn't have. Gates himself may even be tapped by Obama to continue on the job into the new Administration.

As Mullen knows, and as Obama soon will learn, it's never easy guessing where the U.S. military will be needed next. The admiral recently reminded a uniformed audience that at their respective confirmation hearings as Defense Secretary, no one asked Robert McNamara about Vietnam , Dick Cheney about Iraq or Rumsfeld about Afghanistan . "That's how well we predict," he said, ruefully. "And that's not going to change."