The scandal that brought down David Petraeus as head of the CIA seems to grow stranger by the day, with the latest development bringing into the news the man who succeeded Petraeus as Commander of American forces in Afghanistan:

PERTH, Australia — The FBI probe into the sex scandal that prompted CIA Director David Petraeus to resign has expanded to ensnare Gen. John R. Allen, the commander of U.S. and NATO troops in Afghanistan, the Pentagon announced early Tuesday.

According to a senior U.S. defense official, the FBI has uncovered between 20,000 and 30,000 documents — most of them e-mails — of “potentially inappropriate” communications between Allen and Jill Kelley, a 37-year-old Tampa woman whose close relationship with Petraeus ultimately led to his downfall.

Allen, a Marine, succeeded Petraeus as the top allied commander in Afghanistan in July 2011. He also served as Petraeus’s deputy when both generals led the military’s Tampa-based Central Command from 2008 until 2010.

The FBI first notified the Pentagon of its investigation into Allen’s communications with Kelley on Sunday evening, according to the senior defense official, who spoke on condition of anonymity to discuss details of the pending case.

In response, Pentagon chief Leon E. Panetta referred the investigation on Monday to the Defense Department’s Inspector General for further review, according to a statement released by Panetta early Tuesday as he was traveling to Australia.

The latest development in the unfolding scandal has shaken President Obama’s national-security staff and upended his carefully chosen plans for filling senior military and intelligence leadership jobs in his second term.

It also further calls into question the personal behavior of two of the U.S. military’s highest-ranking and most respected figures, who apparently ignored concerns about the highly sensitive nature of their positions as they embraced personal relationships with younger women who were not their wives.

Petraeus’s fall from grace shocked the CIA but especially stunned his former colleagues in the Army, where he was considered one of the most brilliant and influential commanders of his generation. Allen, a Marine, was likewise seen as an intellectual and upstanding role model who first made his mark as a general in Iraq during the George W. Bush administration and later earned Obama’s confidence.

In his statement, Panetta said Allen would remain as commander of U.S. and NATO forces in Afghanistan for now, “while the matter is under investigation and before the facts are determined.” The senior defense official said Allen “disputes that he has engaged in any wrongdoing,” but would not elaborate.

But his time as commander in Afghanistan may be short. Panetta has also asked the Senate to expedite the confirmation of his likely successor, Marine Gen. Joseph F. Dunford.

Obama had nominated Dunford last month to replace Allen. Coincidentally, the Senate Armed Services Committee had already scheduled his confirmation hearing for Thursday. Panetta said he has asked the Senate to expedite its review of Dunford’s nomination.

Allen had been simultaneously nominated by the White House to take over as chief of the military’s European Command and NATO’s Supreme Allied Commander in Europe. That nomination is now on hold, Panetta said, pending the outcome of the probe of his communications with Kelley.

Late last night, the White House announced that it had placed Allen’s nomination to be NATO Commander on hold pending the investigation, suggesting that yet another top General may be taken down in this whole bizarre mess.

As if that weren’t enough, we also learned last night that the FBI Agent who had originally brought Jill Kelley’s “threatening emails” to the attention of the Bureau’s Cyber Crimes unit is now under investigation himself for sending shirtless pictures of himself to Mrs. Kelley:

WASHINGTON—A federal agent who launched the investigation that ultimately led to the resignation of Central Intelligence Agency chief David Petraeus was barred from taking part in the case over the summer due to superiors’ concerns that he was personally involved in the case, according to officials familiar with the probe

After being blocked from the case, the agent continued to press the matter, relaying his concerns to a member of Congress, the officials said.

New details about how the Federal Bureau of Investigation handled the case suggest that even as the bureau delved into Mr. Petraeus’s personal life, the agency had to address conduct by its own agent—who allegedly sent shirtless photos of himself to a woman involved in the case prior to the investigation.

The FBI agent who started the case was a friend of Jill Kelley, the Tampa woman who received harassing, anonymous emails that led to the probe, according to officials. Ms. Kelley, a volunteer who organizes social events for military personnel in the Tampa area, complained in May about the emails to a friend who is an FBI agent. That agent referred it to a cyber crimes unit, which opened an investigation.

However, supervisors soon became concerned that the initial agent might have grown obsessed with the matter, and prohibited him from any role in the investigation, according to the officials.

One official said the agent in question sent shirtless photos to Ms. Kelley well before the email investigation began, and FBI officials only became aware of them some time later. Eventually, supervisors told the agent he was to have nothing to do with the case, though he never had a formal role in the investigation, the official said.

The agent, after being barred from the case, contacted a member of Congress, Washington Republican David Reichert, because he was concerned senior FBI officials were going to sweep the matter under the rug, the officials said. That information was relayed to top congressional officials, who notified FBI headquarters in Washington.