Pentagon ponders transition in time of war

They also believe that all national security personnel should be kept in place until their replacements can be sworn in. Typically, political appointees begin to leave toward the end of an administration, leaving a void that normally has only a small effect.

But it will be largely up to Congress to put its partisan differences aside, she says. "They all talk about wanting a smooth transition, they all say the right things," says Flournoy. "The question is, are they willing to put their money where their mouth is … to make it work."

It will also be incumbent upon the new administration, regardless of political stripe, to approach the Pentagon carefully, says one retired senior military official who was on active duty when President Clinton won the White House as well as when President George Bush won it eight years later.

There were stark differences in the way the two administrations took over, he says. "The team that came in [under Clinton] basically trusted the institutional loyalty of those of us who were in the continuous jobs and so they felt that we were telling them the truth and that we weren't spinning things and giving them bad analysis," says the retired official. By contrast, Secretary Rumsfeld "didn't take advantage" of institutional knowledge from the start.

There was much talk of "Clinton generals," he says, betraying a political mindset toward the military that was ultimately detrimental to defense policy. "Some administration's civilians don't understand institutional loyalty, they only understand personal loyalty."

A longer tour for Gates?

Meanwhile, Gates's reputation for demanding accountability without trumpeting his own personality is popular across the department and in Congress, too. "I think he may be the best secretary of defense we ever had," says one active-duty Army officer in high-level circles.

Now, some would like him to stay on. One respected website devoted to irregular warfare called the Small Wars Journal contains an open letter to the new administration asking that whoever wins to consider keeping Gates.

And David Abshire, president of the Center for the Study of the Presidency, speculates that Gates, while reluctant to stay, could remain in the Pentagon for a time. "I think that he would [consider] staying on, he might answer the call of duty that brought him here in the first place and stay on a year, that's what we need."

But Gates, who carries in his briefcase a special clock that counts down the days he has left in office, has made it clear he wouldn't stay. At the same time, Gates has left the door open ever so slightly with regard to being asked and accepting an extension of his appointment.

"I think he's pretty adamant about it," says another senior Pentagon official in uniform. Regardless of how many openings there might be in a new administration early next year, the official believes there will be a new cabinet member heading the Pentagon from Day 1.

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