The atmosphere of crisis in Washington triggered by retired Gen. David Petraeus’ resignation as CIA director following an FBI investigation into an extramarital affair has deepened with Petraeus’ successor as the top US commander in Afghanistan, Gen. John Allen, being linked to the scandal.

The Obama administration announced Tuesday that it has placed on hold Allen’s nomination to become the senior military commander in NATO and chief of US forces in Europe, following allegations that the American general had engaged in “inappropriate communications”—some 20,000 to 30,000 pages of emails over the last two years—with the woman in Tampa, Florida whose complaint to the FBI initiated the probe that led to Petraeus.

The Pentagon did not clarify what was “inappropriate” about the emails, raising questions as to whether they were of a sexual or security character. An unnamed senior Defense Department official told the Times, however, that the content of some of the e-mails “was of a flirtatious nature.”

The matter is being dealt with by the inspector general’s office of the Department of Defense. Under some circumstances, adultery is a prosecutable offense under the Uniform Code of Military Justice. While Obama issued a statement praising Allen for “ably” leading American occupation troops in Afghanistan, the administration also pressed the Senate to hold speedy confirmation hearings for the officer nominated to succeed Allen in Kabul, Gen. Joseph Dunford.

The woman to whom Allen had allegedly sent the emails was Jill Kelley, a Tampa socialite and wife of a local doctor. Last June, Kelley contacted a personal friend in the Tampa FBI office complaining of harassing emails from an anonymous source.

The FBI launched an investigation and traced the harassing emails to Paula Broadwell, a married US Army reserve officer and West Point graduate, who had authored a fawning biography of Gen. Petraeus that was published last January. The investigation, according to the FBI’s account, led to the discovery of extensive emails between Broadwell and Petraeus and subsequent interviews in which both acknowledged the affair.

A senior Pentagon official told the AFP news agency that there was a “distinct possibility” that the emails between Allen and Kelley were linked to Petraeus. Allen has denied any wrongdoing.

Kelley, 37, had become a self-styled and unpaid “social liaison” to McDill Air Force base in Tampa, the headquarters of Central Command, which oversees American military operations in the Middle East and Central Asia. Petraeus headed Central Command from 2008 to 2010. During the same period, General Allen was deputy commander of Central Command. He took over as commander in 2010 when Petraeus was tapped to head US forces in Afghanistan, and then succeeded Petraeus in Afghanistan when the latter was named by Obama to head the CIA.

The emails sent anonymously by Broadwell to Kelley reportedly appeared to be motivated by jealousy and included warnings to Kelley to stay away from Petraeus. Associates of Petraeus have insisted that Kelley and her husband were only family friends.

It was reported Tuesday that Kelley has hired Abbe Lowell, the attorney who defended President Bill Clinton during impeachment proceedings, as well as Judy Smith, the Washington, DC “crisis manager” who has represented clients ranging from Monica Lewinsky to Enron.

Meanwhile, the FBI is reportedly conducting its own investigation into the agent whom Kelley originally contacted. He had been ordered by his superiors to stay away from the case, with which he appeared to be personally obsessed, according to a report published Tuesday in the Wall Street Journal. According to this account, FBI officials learned that the agent had sent shirtless photographs of himself to Kelley well before the investigation was initiated.

Apparently convinced that the FBI was conducting a cover-up of the Broadwell-Petraeus affair, the agent went to a Republican member of Congress, David Reichert of Washington. Reichert passed the information along to senior Republicans, including House Majority Leader Eric Cantor of Virginia, who in turn alerted the FBI to the leak, but kept the fact of the investigation of Petraeus secret.

Involving two highly secretive US intelligence agencies and now the top military command, the scandal obviously has deep-going political dimensions and has raised a host of questions that remain unanswered.

First, it is by no means clear why the FBI initiated such an investigation into what was by any measure a routine case of cyber-stalking in which few police agencies would take any interest. According to the Journal, FBI officials claim that when the investigation began, it was not clear that the harassing emails concerned Petraeus.

Then there is the issue of the failure of the FBI to inform either the White House or the leaders of congressional intelligence committees of the investigation of the CIA director. According to the official story, Director of National Intelligence James Clapper was told of the investigation of Petraeus, which began last June, only on Election Day, while President Obama wasn’t informed until November 8, two days after he won reelection.

The FBI’s claim that it had no obligation to notify the White House or the relevant committees in Congress as the investigation concerned cybercrime rather than intelligence strains credulity. Once it was clear that the probe involved the director of the CIA, it was clearly an intelligence matter.

It has also been reported that Attorney General Eric Holder learned of the investigation last summer, but supposedly failed to inform the president.

It would seem that either the Obama administration decided to suppress the matter until after the election was over, or the FBI decided to pursue the matter on its own and keep it from the White House for reasons that are not clear. There have long been sharp tensions and turf wars between the FBI and the CIA.

Dianne Feinstein, the Democratic senator from California who chairs the Senate Intelligence Committee, has vowed that her committee will conduct an investigation into why the FBI did not inform the panel of the probe, given that by law it is required to keep leaders of the House and Senate intelligence committees apprised of investigations that could have an impact on national security.

Also open to question is the FBI’s assertion that it had concluded early on there was no evidence that Paula Broadwell had improperly received classified information from the CIA director, even though secret documents were found on her computer during the investigation. Moreover, it is apparent that the investigation is continuing, as FBI agents searched Broadwell’s North Carolina home Monday night, carting off boxes of documents.

Broadwell has herself boasted of unique access to intelligence secrets because of her connection to Petraeus. During a panel discussion at the Aspen Security Forum last July, she said, “I was entrusted with this opportunity to sit in on high-level meetings with General Petraeus. Sitting in on SCIF [sensitive compartmented information facility] meetings in the morning, listening to classified chatter on terrorist talk and so forth.”

Also, in a speech delivered last month at the University of Denver, Broadwell provided previously undisclosed information about the September 11 attack on the US consulate and the secret CIA facility in Benghazi, Libya that claimed the lives of the US ambassador and three other Americans.

“I don't know if a lot of you have heard this, but the CIA annex had actually taken a couple of Libyan militia members prisoner and they think that the attack on the consulate was an effort to get these prisoners back,” she said.

Broadwell also spoke with some specificity in identifying the special operations unit that was initially called upon to respond to the Benghazi attack, describing it as “a group of Delta Force operators.” In the same remarks, Broadwell cited Petraeus, saying that “he had correspondence with the CIA station chief in Libya. Within 24 hours, they kind of knew what was happening.”

A CIA spokesman categorically denied that the agency had held detainees at the Benghazi facility.

Petraeus had been scheduled to testify before the Senate Intelligence Committee on the Benghazi attack this week. While initially it was reported that after resigning he would not appear, the committee’s chair, Senator Feinstein, said Tuesday that she is moving ahead to set up a closed-door hearing with the ex-CIA director as early as Friday.

Speaking to the New York Daily News, Paula Broadwell’s father, Paul Krantz, suggested that the story about an extra-marital affair between his daughter and Petraeus was being used as a smokescreen to cover up a deeper crisis.

“This is about something else entirely, and the truth will come out,” he said. “There is a lot more that is going to come out. You wait and see. There’s a lot more here than meets the eye.”