Widening Petraeus scandal comes at already troublesome time for Pentagon

Gen. John Allen, commander of US forces in Afghanistan, is under investigation by the Department of Defense, as part of the inquiry into David Petraeus's affair. The Pentagon already had big personnel moves planned, and budget questions loom.

News of the latest figure in the widening soap opera that is a Federal Bureau of Investigation inquiry – now involving Gen. John Allen, the commander of US forces in Afghanistan – comes at a particularly troublesome time for the Pentagon.

At 1:30 a.m. Tuesday, Defense Secretary Leon Panetta’s office released a statement via BlackBerry confirming that Allen, who took the top job in Kabul after David Petraeus moved to the Central Intelligence Agency in September 2011, is now under investigation by the Department of Defense. This scrutiny is the result of an FBI referral. 

For now, Allen will remain commander in Afghanistan. 

“His leadership has been instrumental in achieving the significant progress that [the International Security Assistance Force], working alongside our Afghan partners, has made in bringing greater security to the Afghan people and in ensuring that Afghanistan never again becomes a safe haven for terrorists,” Secretary Panetta said in his statement. “He is entitled to due process in this matter.”

What precisely “this matter” is remains the topic of much speculation within the halls of the Pentagon. What is known is that the FBI found between 20,000 and 30,000 “potentially inappropriate” e-mails between Allen and Jill Kelley, the Tampa, Fla., socialite who was the recipient of harassing e-mails from Paula Broadwell, the biographer and paramour of Mr. Petraeus.

Officials point out that “inappropriate” e-mails does not necessarily mean risqué or classified. Allen, according to Pentagon officials, “disputes that he has engaged in any wrongdoing.” 

That said, Panetta asked President Obama to put on hold Allen’s nomination to become Supreme Allied commander, Europe, pending the investigation of the Pentagon’s Office of Inspector General. 

As to questions about whether Petraeus’s affair did indeed begin after he left his post in Afghanistan, as his former closest advisers insist, Panetta told reporters, “I’m reading the papers just like you are.”

Allen’s confirmation hearing had been scheduled to take place before the Senate Armed Services Committee on Thursday morning.

Panetta has already named Gen. Joseph Dunford, currently the No. 2 officer in the Marine Corps, to succeed Allen. Panetta urged Congress to expedite that confirmation.

Allen had been expected to give some indication of the state of America’s war in Afghanistan during his testimony Thursday. 

The developments leave growing uncertainty in some of the highest defense posts in the United States.

Allen has been at the center of the process to determine how many US troops should leave Afghanistan – and how many should stay – through 2014 and beyond. Currently 68,000 US troops are in the country.

That process, Panetta said Monday, was nearly complete, and he said he hoped the Pentagon would be able to have some answers in the next few weeks. “General Allen has worked on several options that we are now reviewing and working with the White House on,” he said.

Panetta, who is traveling to Australia for security meetings this week, for his part is widely expected to step down as secretary of Defense now that Mr. Obama’s first term is complete. 

He declined to shed any light on his retirement plans when asked about them during an in-flight press conference Monday. 

“Who the hell knows?” he said. “It’s no secret that at some point, I’d like to get back to California. It’s my home.” 

Panetta also gave some indication of his frustration surrounding the highest echelons of military leadership in comments about the threat of sequestration, the automatic series of budget cuts slated to take effect if Congress doesn’t act by January. 

“That's the last damn thing I need right now, is to have more uncertainty,” he said.

On whether he would step down before year’s end or, as is widely expected, after the Pentagon’s budget hearings early year, Panetta responded in what could be read as a parable for the national security community’s latest crisis.

“My experience in Washington,” he said, “is you better do this day to day.”