TAMPA, Florida (AP) -- CIA Director David Petraeus was shocked to learn last summer that his mistress was suspected of sending threatening emails warning another woman to stay away from him, former staff members and friends told the Associated Press.

Petraeus, who led U.S. military efforts in Iraq and Afghanistan, resigned his CIA post Friday, acknowledging his extramarital affair with his biographer-turned-lover and expressing deep regret. The scandal has rocked Washington, where members of Congress demanded to know why a months-long probe that ended the former general’s storied career was kept quiet for so long.

Petraeus told associates his relationship with the second woman, Tampa socialite Jill Kelley, was platonic, though his lover Paula Broadwell apparently saw her as a romantic rival. The retired general also denied to these associates that he had given Broadwell any of the sensitive military information alleged to have been found on her computer, saying anything she had must have been provided by other commanders during her reporting trips to Afghanistan.

The associates spoke Monday on condition of anonymity because they weren’t authorized to publicly discuss the matters, which could be part of an FBI investigation.

Meanwhile, the Pentagon said Tuesday that the top American commander in Afghanistan, Gen. John Allen, is under investigation for alleged “inappropriate communications” with Kelley.

A senior defense official, who discussed the matter only on condition of anonymity because it is under investigation, said 20,000 to 30,000 pages of emails and other documents from Allen‘s communications with Kelley between 2010 and 2012 are under review by the Pentagon. He would not say whether they involved sexual matters or whether they are thought to include unauthorized disclosures of classified information. The official said Allen has denied any wrongdoing.

FBI agents appeared at Broadwell’s Charlotte, North Carolina, home Monday night and appeared to be conducting a search. An FBI spokeswoman confirmed the agents’ presence but did not say what they were doing.

New details of the investigation emerged as President Barack Obama hunted for a new CIA director.

Kelley, the Tampa woman, began receiving harassing emails in May, according to two federal law enforcement officials. They, too, spoke only on condition of anonymity because they were not authorized to speak publicly about the matter. The emails led Kelley to report the matter, eventually triggering the investigation that led Petraeus to resign as head of the intelligence agency.

FBI agents traced the alleged cyber harassment to Broadwell, the officials said, and discovered she was exchanging intimate messages with a private gmail account. Further investigation revealed the account belonged to Petraeus under an alias.

Petraeus and Broadwell apparently used a trick, known to terrorists and teenagers alike, to conceal their email traffic, one of the law enforcement officials said.

Rather than transmitting emails to the other’s inbox, they composed at least some messages and instead of transmitting them, left them in a draft folder or in an electronic “dropbox,” the official said. Then the other person could log onto the same account and read the draft emails there. This avoids creating an email trail that is easier to trace.

Broadwell had co-authored a biography titled “All In: The Education of General David Petraeus,” published in January. In the preface, she said she had met Petraeus in the spring of 2006 while she was a graduate student at the Kennedy School of Government at Harvard and she ended up following him on multiple trips to Afghanistan as part of her research.

But the contents of the email exchanges between Petraeus and Broadwell suggested to FBI agents that their relationship was intimate. The FBI concluded relatively quickly -- by late summer at the latest -- that no security breach had occurred, the two senior law enforcement officials said. But the FBI continued its investigation into whether Petraeus had any role in the harassing emails.

Petraeus, 60, told one former associate he began an affair with Broadwell, 40, a couple of months after he became the director of the CIA late last year. They mutually agreed to end the affair four months ago, but they kept in contact because she was still writing a dissertation on his time commanding U.S. troops overseas, the associate said.

FBI agents contacted Petraeus, and he was told that sensitive, possibly classified documents related to Afghanistan were found on her computer. He assured investigators they did not come from him, and he mused to his associates that they were probably given to her on her reporting trips to Afghanistan by commanders she visited in the field there. The FBI concluded there was no security breach.

One associate also said Petraeus believes the documents described past operations and had already been declassified, although they might have still been marked as “secret.” Broadwell had high security clearances on her own as part of her job as a reserve Army major working for military intelligence. But those clearances are only in effect when a soldier is on active duty, which she was not at the time she researched the Petraeus biography.

During a talk last month at the University of Denver, Broadwell caught attention when she said the CIA had detained people at a secret facility in Benghazi, Libya, and the Sept. 11 attack on the U.S. Consulate and CIA base there was an effort to free those prisoners.

Obama issued an executive order in January 2009 stripping the CIA of its authority to take prisoners. The move meant the CIA was forbidden from operating secret jails across the globe as it had under President George W. Bush.

CIA spokesman Preston Golson said: “Any suggestion that the agency is still in the detention business is uninformed and baseless.”

Broadwell did not say who told her about CIA activities in Libya. The video of Broadwell‘s speech was viewed on YouTube.

A Petraeus associate said the retired general was shocked to find out about Broadwell’s emails to Kelley. Petraeus was not shown the messages, but investigators told him the emails told Kelley to stay away from the general in a threatening tone.

Petraeus told former staffers and friends that he was friends with Kelley and her surgeon husband, Scott, and regularly visited their brick home with imposing white columns overlooking Tampa Bay.

Jill Kelley, 37, served as a sort of social ambassador for U.S. Central Command, hosting parties for the general when Petraeus was commander there from 2008-2010.