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

At 1:30 a.m. Tuesday, Defense Secretary Leon Panetta鈥檚 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.聽

For now, Allen will remain commander in Afghanistan.聽

鈥淗is 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,鈥� Secretary Panetta said in his statement. 鈥淗e is entitled to due process in this matter.鈥�

What precisely 鈥渢his matter鈥� 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 鈥減otentially inappropriate鈥� 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 鈥渋nappropriate鈥� e-mails does not necessarily mean risqu茅 or classified. Allen, according to Pentagon officials, 鈥渄isputes that he has engaged in any wrongdoing.鈥澛�

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

As to questions about whether Petraeus鈥檚 affair did indeed begin after he left his post in Afghanistan, as his former closest advisers insist, Panetta told reporters, 鈥淚鈥檓 reading the papers just like you are.鈥�

Allen鈥檚 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鈥檚 war in Afghanistan during his testimony Thursday.聽

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 鈥� and how many should stay 鈥� through 2014 and beyond. Currently 68,000 US troops are in the country.

That process,聽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. 鈥淕eneral Allen has worked on several options that we are now reviewing and working with the White House on,鈥� 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鈥檚 first term is complete.聽

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

鈥淲ho the hell knows?鈥� he said. 鈥淚t鈥檚 no secret that at some point, I鈥檇 like to get back to California. It鈥檚 my home.鈥澛�

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鈥檛 act by January.聽

鈥淭hat's the last damn thing I need right now, is to have more uncertainty,鈥� he said.

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

鈥淢y experience in Washington,鈥� he said, 鈥渋s you better do this day to day.鈥�