By Mike Mount, CNN Senior National Security Producer
The fallout from the scandal involving now disgraced CIA Director Gen. David Petraeus and possible connection to top Afghan commander Gen. John Allen comes at a transition time for the Obama administration. Just a week after the election, one of Washington's favorite guessing games started as politicians, journalists and every other political wonk started to calculate who could be filling the major Cabinet positions that would be opening as some get set to step down. It raises the question of what effect all this could have on the country's national security.
Secretary of State Hillary Clinton long ago announced she would be leaving and Secretary of Defense Leon Panetta, said this week that he does want to return to his home in California. Asked how long he plans to stick around the Pentagon, he responded to reporters, "Who the hell knows?"
In the military, regularly scheduled command changes were getting set as well, as Allen was moving to head the European Command and a new commander was preparing to take over in Afghanistan. Both have to be confirmed by the Senate and a confirmation hearing is set for Thursday with the Senate Armed Services Committee.
But in light of the scandal, is the president at risk of losing too much of his foreign policy brain trust as Petraeus departs and Allen works under the haze of an investigation?
White House spokesman Jay Carney addressed that question Tuesday, saying the president, "has great confidence in the acting CIA director. He has confidence in his military, and the secretary of Defense and the Defense Department to carry out the missions that he has assigned to them."
Mark Jacobson, a former NATO adviser to Petraeus while he was in Afghanistan and now a fellow at the policy analysis group The German Marshall Fund, says a scandal like this would not affect national security.
"What it is, is a loss for the CIA, which does need some restructuring, as does the Pentagon, Defense Intelligence Agency and the National Security Agency. Folks need to move away from Afghanistan and Iraq and start looking at the long-term strategic picture and I think Petraeus was the right guy to do that for the agency," Jacobson said.
"There was a thought he (Petraeus) could be leaving to head up Princeton this year, so he might have left anyhow," Jacobson said.
But if the personal nature of the relationship between Petraeus and his biographer, Paula Broadwell, does not have a consequence on national security, surely the decision-making process of who will fill the open positions could have a trickle down effect.
For instance, if the Obama administration loses its top CIA boss and its top commander in Afghanistan, on top of the departure of Clinton and the expected departure of Panetta, who could possibly oversee the sensitive diplomatic and military mission of the final two years of U.S. troops in Afghanistan?
Surprisingly, many in Washington think there are plenty of qualified people who can fill these gaps. In fact, many national security staffers on Capitol Hill we spoke with Tuesday believe the scandal will not hollow out those with national security experience in the administration.
"It's not like there is a void of qualified people. If that was the case the president would have to keep Petraeus in his job," said one Capitol Hill staffer who asked not to be identified.
But one senior Hill staffer thinks the Pentagon's decision to not outright fire Allen and keep him in his position is not only a signal that the military does not know if he was in the wrong, but also a way to protect him if he is found not to be at fault.
"It would be a shame to lose a man with the experience he has in Afghanistan if they were to fire him only to find that he was not actually guilty of anything," the staffer said.
But even keeping Allen in the role he was expected to be confirmed for as head of the U.S. European Command, who could fill the other gaps in higher positions?
The CIA No. 2 man under Petraeus, Mike Morell, has been in that position for years and knows just as much about Afghanistan and Libya and numerous other hot spots than anyone.
Other names, like former Rep. Jane Harman, a stalwart on national security issues, is also somebody whose name is often mentioned. The names being whispered now were being whispered before this scandal broke. The same goes for the Pentagon. Jacobson says a decision there would be driven by the possible large-scale budget cuts.
Sen. John Kerry, D-Massachusetts and head of the Senate Foreign Relations Committee, has been bounced around as a possible secretary of state or secretary of defense. Susan Rice, the U.S. ambassador to the United Nations, has support inside the administration to head the State Department.
"The shuffle will largely be unaffected by it (the scandal)," Jacobson said. "I think the administration has some time to maneuver, and some might say this gives the president another position to be able to fill."
The White House is still playing its hand close to its chest when asked if the president will revamp his national security team.
"I can tell you that the president has not made decisions on personnel matters, and you will not hear me discuss them until the president has made those decisions and has announced them," White House spokesman Jay Carney told reporters Tuesday.
Allen is working on options to present to the White House regarding the U.S. presence in Afghanistan after the withdrawal of most troops in 2014. But even with that key job, Allen already had one foot out the door.
"I'm not sure it (the scandal) has a big national security impact in Afghanistan. ... I think there are bigger drivers on that right now," Jacobson said. "This is about the White House foreign policy agenda and the Afghans being more helpful and providing an atmosphere where ISAF forces can operate," he said.
There are bigger problems with the Afghans that must be addressed and a lot of political wrangling going on just below the surface with a lack of cooperation by the Afghans.
"If the Afghans are less cooperative, then the administration is less likely to listen to arguments about why we should slow the pace of the withdrawal," he said.
But as investigations ramp up and look to see if any damage to national security has been done, Republicans maintain that the Petraeus departure is only part of a bigger picture that ties the scandal to the attacks in Benghazi, Libya.
As more information comes out on the September 11 attack there it is becoming more clear that Petraeus knew much more about what happened than has been said by the Obama administration.
Closed hearings on Capitol Hill scheduled for this week will begin to dive into what happened and who knew what when.