Even as the FBI prepared a timeline for Congress about the investigation that brought to light Petraeus' extramarital affair with his biographer, Paula Broadwell, Defense Secretary Leon Panetta revealed that the Pentagon had begun an internal investigation into emails between Gen. John Allen and a Florida woman involved in the case.
Some of the 20,000-plus pages of documents and emails between Allen and Tampa socialite Jill Kelley were "flirtatious," according to a senior defense official who spoke on condition of anonymity because he wasn't authorized to discuss the case publicly. It wasn't immediately clear who wrote the flirtatious notes—Allen, Kelley or both.
Allen succeeded Petraeus as the top American commander in Afghanistan in July 2011, and his nomination to become the next commander of U.S. European Command and the commander of NATO forces in Europe has now been put on hold, as the scandal seemed certain to ensnare another acclaimed military figure.
In a White House statement early Tuesday, National Security spokesman Tommy Vietor said President Barack Obama has held Allen's nomination at Panetta's request.
It was Broadwell's threatening emails to Kelley, a Petraeus family friend, that led to the FBI's discovery of communications between Broadwell and Petraeus indicating they were having an affair. Petraeus acknowledged the affair when he resigned from the CIA post on Friday.
In the latest revelations, a Pentagon official traveling with Panetta to Australia said "inappropriate communications"—20,000 to 30,000 pages of emails and other documents from Allen's communications with Kelley between 2010 and 2012—are under review. The official would not say whether they involved sexual matters or whether they are thought to include unauthorized disclosures of classified information. He said he did not know whether Petraeus is mentioned in the emails.
Allen has denied wrongdoing. He was due to give Panetta a recommendation soon on the pace of U.S. troop withdrawals in 2013. If Allen was found to have had an affair with Kelley, he could face charges of adultery, which is a crime under the Uniform Code of Military Justice.
The decision by the FBI to hand off the Allen information to the military seems to indicate the issue is not one involving the handling of classified information, but rather some other issue.
The Petraeus case has sparked an uproar in Congress, with lawmakers complaining they should have been told earlier about the probe that has roiled the intelligence and military establishment.
Rep. Peter King, R-N.Y., chairman of the House Homeland Security Committee, called the latest revelations in the case "a Greek tragedy."
"It's just tragic," King said Tuesday on NBC's "Today" show. "This has the elements in some ways of a Hollywood movie or a trashy novel."
The issue of what the FBI knew, when it notified top Obama administration officials, and when Congress was told, has brought criticism from lawmakers, who say they should have been told earlier.
The White House wasn't informed of the FBI investigation that involved Petraeus until Nov. 6, Election Day, although agents began looking at Petraeus' actions months earlier, sometime during the summer. Senate Intelligence Committee chairwoman Dianne Feinstein, D-Calif., complained that she first learned of the matter from the media late last week, and confirmed it in a phone call to the then-CIA director on Friday.
That was the same day Obama accepted Petraeus' resignation, and the 60-year-old retired Army general, who headed U.S. military operations in Iraq and Afghanistan before taking charge of the CIA, acknowledged an affair with Broadwell, and expressed regret.
Defending the notification timing, a senior federal law enforcement official pointed Monday to longstanding policies and practices, adopted following abuses and mistakes that were uncovered during the Nixon administration's Watergate scandal of the early 1970s. The Justice Department—of which the FBI is part—is supposed to refrain from sharing detailed information about its criminal investigations with the White House.
The FBI also looked into whether a separate set of emails between Petraeus and Broadwell might involve any security breach. That will be a key question Wednesday in meetings involving congressional intelligence committee leaders, FBI deputy director Sean Joyce and CIA deputy director Michael Morell.
A federal law enforcement official, speaking on condition of anonymity to discuss details of the investigation, said the FBI had concluded relatively quickly—and certainly by late summer at the latest—that there was no security breach. Absent a security breach, it was appropriate not to notify Congress or the White House earlier, this official said.
Extramarital affairs are viewed as particularly risky for intelligence officers because they might be blackmailed to keep the affair quiet. For military personnel, adultery is a crime under the Uniform Code of Military Justice.
According to two federal law enforcement officials, the FBI initially began a criminal investigation of unsigned, harassing emails that were sent, beginning last May, to Kelley, a Tampa socialite. She and her husband, Scott, were longtime friends of Petraeus and his wife, Holly. FBI agents traced the alleged cyber harassment to Broadwell and during that process discovered she was exchanging intimate messages with a private Gmail account. Further investigation revealed that 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 for outsiders to intercept or trace.
Agents later told Petraeus that Broadwell sent emails warning Kelley to stay away from the general and carrying a threatening tone.
Friends and former staff members of Petraeus told The Associated Press that he has assured them his relationship with Kelley was platonic, although Broadwell apparently saw her as a romantic rival. They said Petraeus was shocked to learn last summer of Broadwell's emails to Kelley.
Petraeus also denied to these associates that he had given Broadwell any sensitive military information.
FBI agents who contacted Petraeus told him that sensitive, possibly classified documents related to Afghanistan were found on her computer, the general's associates said. 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.
One associate also said Petraeus believes the documents described past operations and had already been declassified, although they might have still been marked "secret."
Broadwell had high security clearances as part of her former job as a reserve Army major in 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.
The FBI concluded there was no security breach.
Nevertheless, FBI agents conducted a search of Broadwell's Charlotte, N.C., home on Monday. And the criminal investigation continued into the emails to Kelley, including whether Petraeus had any hand in them. At that point in late summer, FBI Director Robert Mueller and eventually Attorney General Eric Holder were notified that agents had uncovered what appeared to be an extramarital affair involving Petraeus.
Broadwell and Petraeus have each been questioned by FBI agents twice in recent weeks, with both acknowledging the affair in separate interviews. The FBI's most recent interviews with Broadwell and with Petraeus both occurred during the week of Oct. 29, days before the election, one of the law enforcement officials said. The FBI notified Obama's director of national intelligence, James Clapper, of the investigation on Tuesday, Nov. 6—Election Day.
In another twist, an FBI agent who was a friend of Kelley and who passed along information from her to the agents who conducted the investigation, was subsequently told by his superiors to steer clear of the case because they grew concerned that the agent had become obsessed with the investigation, a federal law enforcement official said. Before the case involving Petraeus got under way, the agent had sent Kelley shirtless photos of himself, according to this official, who spoke on condition of anonymity to discuss the investigation.
Broadwell co-authored a biography titled "All In: The Education of General David Petraeus," published in January. She wrote that she 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.
Petraeus, 60, told one former associate he began an affair with Broadwell, 40, a couple of months after he became CIA director in September 2011. 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.
Petraeus told former staffers and friends that he had regularly visited the Kelleys' home overlooking Tampa Bay. 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 2008-10.
Jill Kelley regularly kept in touch with Petraeus when he became commander of the Afghanistan war effort, the two exchanging near-daily emails and instant messages, two of his former staffers said. But those messages were exchanged in accounts that his aides monitored as part of their duties and were not romantic in tone, the staffers said.
Petraeus and his family are devastated over the affair—especially Mrs. Petraeus, who "is not exactly pleased right now" after 38 years of marriage, said Steve Boylan, a friend and former Petraeus spokesman who spoke to him over the weekend.
Broadwell, married with two young sons, has not returned phone calls or emails seeking comment.
National Security writer Robert Burns reported from Perth, Australia. Associated Press writers Pauline Jelinek, Nedra Pickler, Larry Margasak and Adam Goldman contributed from Washington.