WASHINGTON — The FBI investigation that led to the resignation of David Petraeus as CIA director Friday began with a complaint several months ago about “harassing” e-mails sent by Paula Broadwell, Petraeus’ biographer, to an unidentified third person, a government official briefed on the case said Saturday.
When FBI agents following up on the complaint began to examine Broadwell’s e-mails, they discovered exchanges between her and Petraeus that revealed they were having an affair, said the official, who spoke of the investigation on the condition of anonymity.
The person who complained about harassing messages from Broadwell, the official said, was not a family member or a government official. One congressional official who was briefed on the matter Friday said senior intelligence officials had explained that the FBI investigation “started with two women.”
“It didn’t start with Petraeus, but in the course of the investigation they stumbled across him,” said the congressional official, who said the intelligence officials had provided no other information about the two women or the focus of the inquiry. “We were stunned.”
Petraeus said in a statement that he was resigning after 14 months as head of the Central Intelligence Agency because he had shown “extremely poor judgment” in engaging in the affair.
Petraeus has been married for 38 years to Holly Petraeus, the daughter of the West Point superintendent when he was a student at the New York school.
“He is truly remorseful about everything that’s happened,” said Steve Boylan, a retired Army officer and former Petraeus spokesman who spoke with the former general Saturday. In a phone call with Boylan on Saturday, Petraeus lamented the damage he’d done to his “wonderful family” and the hurt he’d caused his wife.
“He screwed up, he knows he screwed up, now he’s got to try to get past this with his family and heal,” said Boylan.
Neither the congressional intelligence committees nor the White House learned of the investigation or the link to Petraeus until last week, officials said. Neither did Petraeus’ boss, James Clapper, the director of national intelligence.
A senior intelligence official said Saturday that Clapper had learned of Petraeus’ situation only when the FBI notified him about 5 p.m. Tuesday. That night and the next day, the official said, the two men discussed the situation and Clapper told Petraeus “that he thought the right thing to do would be to resign,” the intelligence official said.
Clapper notified the president’s senior national security staff late Wednesday that Petraeus was considering resigning because of an extramarital affair, the official said.
Some congressional staff members said they believed the bureau should have informed at least the Republican and Democratic leaders of the House and Senate intelligence committees about the unfolding inquiry. The committees are likely to demand an explanation of why they were not told.
“Why didn’t the FBI tell us?” said Rep. Peter King, a New York Republican on the House Intelligence Committee. “Why was the FBI investigating the CIA — and this was involving a compromised computer of the director of the CIA, nobody told the president or the White House?”
White House officials said they were informed Wednesday night that Petraeus was considering resigning. On Thursday morning, just before a staff meeting at the White House, Obama was told.
That afternoon, Petraeus went to see him and informed him that he strongly believed he had to resign. Obama did not accept his resignation right away, but on Friday, he called Petraeus and accepted it.
CIA Deputy Director Michael Morell took over as acting director with Petraeus’ departure, Obama said. The president said he was “completely confident that the CIA will continue to thrive and carry out its essential mission.”
The government official dismissed a range of media speculation that the FBI inquiry might have focused on leaks of classified information to reporters or even foreign spying. “People think that because it’s the CIA director, it must involve bigger issues,” the official said. “Think of a small circle of people who know each other.”
The FBI investigators were not pursuing evidence of Petraeus’ marital infidelity, which would not be a criminal matter, the official said. But their examination of his e-mails, most or all of them sent from a personal account and not from his CIA account, raised the possibility of security breaches that needed to be addressed directly with him.
“Alarms went off on larger security issues,” the official said. As a result, FBI agents spoke with the CIA director about two weeks ago, and he learned in the discussion, if he was not already aware, that they knew of his affair with Broadwell, the official said.
Web-based e-mail like Gmail and Yahoo Mail can be quite vulnerable to hacking, and it is possible that FBI experts were studying whether Petraeus’ accounts had been compromised. Any possibility that hackers could use the CIA director’s e-mail as a route to break into sensitive government computer systems would be an obvious concern.
But the fears of bigger security problems proved unjustified, and the security questions were resolved, the official said.
But there are still several unanswered questions surrounding the circumstances of the FBI investigation and about the affair between Petraeus and Broadwell, officials said Saturday.
It is not clear yet, for instance, when Attorney General Eric Holder or Robert Mueller, the director of the FBI, became aware that the FBI’s investigation into Broadwell’s e-mails had run across Petraeus.
Tracy Schmaler, a spokesman for Holder, declined to comment Saturday on when he was informed about or authorized the surveillance of Petraeus’ e-mails.
The authorities have provided no information about the person who filed a complaint about Broadwell’s e- mail. Broadwell, who is married with two young sons, has not responded to multiple e-mails and phone messages seeking comment.
A graduate of the U.S. Military Academy at West Point, Petraeus retired from the Army in 2011 to take the helm of the CIA. Before that, he stepped in, at Obama’s request, to command the war in Afghanistan after Army Gen. Stanley McChrystal resigned after an embarrassing article in Rolling Stone magazine.
Petraeus, a specialist in counterinsurgency tactics, became well known in Washington circles during his time overseeing and implementing President George W. Bush’s 2007 “surge” of U.S. troops in Iraq. In regular appearances on Capitol Hill, some involving members of Congress questioning both the war strategy and the conflict itself, he garnered support among many lawmakers.
The U.S. Senate, sharply divided along political lines, approved his nomination for CIA director by 94-0 in June 2011.
Dianne Feinstein, a California Democrat who is chairman of the Senate Intelligence Committee, called the resignation “an enormous loss” for the intelligence community and country.
The sudden departure of Petraeus leaves another national security vacancy for Obama to fill, with Secretary of State Hillary Clinton and Defense Secretary Leon Panetta expected to leave sometime next year, possibly along with Clapper.
Morell, who is close to Denis McDonough, the deputy national security adviser, and other members of the National Security Council staff, is a leading candidate to succeed Petraeus, along with Michael Vickers, undersecretary of defense for intelligence, according to administration officials who spoke on the condition of anonymity to discuss possible options.
Another potential candidate, former U.S. Sen. Chuck Hagel, R-Neb., a co-chairman of the President’s Intelligence Advisory Board, has shown no interest in the job.
Commending Petraeus for his “drive and focus” at the agency, Morell said in a statement to CIA employees that “our top priority now is what it always has been — to stay focused on mission and on all the important work we do.”
Information for this article was contributed by Scott Shane, Eric Schmitt, Charlie Savage and Michael S. Schmidt of The New York Times; by Phil Mattingly, John Walcott, Julianna Goldman, Derek Wallbank, Kim Chipman, Jeff Bliss, Michael Shepard, Robin Meszoly and Laura Litvan of Bloomberg News; and by Kimberly Dozier, Pete Yost and Adam Goldman of The Associated Press.
Front Section, Pages 1 on 11/11/2012