Former CIA Director David Petraeus has offered an apology over his affair in an email to a friend, saying Friday night that he was “deeply sorry” for the pain he’s cause the nation and his own family, it was revealed today.

David Petraeus’ long-time friend told the Washington Post that the retired general was extremely sorry over his extramarital affair, allegedly with his biographer, Paula Broadwell.

His apology comes as reports show that David Petraeus’ career could have imploded Paula Broadwell allegedly sent threatening e-mails to another woman she suspected of being too close to him.

In fact, the as-yet unidentified woman could be the key to the entire scandal unfolding after it was claimed she contacted the FBI for protection after receiving frightening emails. Agents traced the threats to Paula Broadwell.

However, it is claimed that Paula Broadwell was using David Petraeus’ own Gmail account to send the emails and when the FBI began to investigate an obvious national security issue instead uncovered explicit messages between the two sent from the decorated war hero’s own account – indicating an affair.

Three senior law enforcement officials with knowledge of the case told the Washington Post that when David Petraeus’s name was raised in connection with the threatening emails the FBI thought that security had been breached.

Beginning their investigation into how the Director of the CIA’s personal email had been hacked, the FBI agents instead uncovered evidence that he and 40-year-old Paula Broadwell were involved in an extramarital affair.

FBI investigators first interviewed David Petraeus about what they had found two weeks ago and informed him that no criminal charges would be brought and no-one is thought to have discussed the possibility of his resignation.

But, according to the Washington Post, after an investigation Justice Department officials were unclear what to do next, because no crime had occurred nor breach of security.

Paula Broadwell allegedly sent threatening e-mails to another woman she suspected of being too close to David Petraeus

They contacted James Clapper, the Director of National Intelligence and told him they had compromising material about David Petraeus.

James Clapper in turn spoke to David Petraeus and advised him to resign.

“Director Clapper learned of the situation from the FBI on Tuesday evening around 5 p.m.,” the intelligence official said to the Washington Post.

“In subsequent conversations with Director Petraeus, Director Clapper advised Director Petraeus to resign.”

Director James Clapper also added that he did not see the need for an internal investigation by the CIA, citing it as “a very personal matter, not a matter of intelligence”.

On Wednesday evening, Director James Clapper went to the White House and on Thursday morning President Barack Obama was informed.

Later on Thursday, David Petraeus arrived to see the President and offered his resignation, which was accepted on Friday.

The Washington Post has also reported that in an email message to a friend, David Petraeus apologized for his actions.

“He was deeply sorry for the pain he has caused his family,” the friend said.

“He also noted how much he loved his job at the agency. He said he really relished the intellectual challenge there.”

Paula Broadwell’s biography, All In: The Education of General David Petraeus, was written with Vernon Loeb, a Washington Post editor, and published in January.

The resignation comes at a sensitive time. The administration and the CIA have struggled to defend security and intelligence lapses before the attack that killed the U.S. ambassador to Libya and three others. It was an issue during the presidential campaign that ended with Barack Obama’s re-election Tuesday.

The CIA has come under intense scrutiny for providing the White House and other administration officials with talking points that led them to say the Benghazi attack was a result of a film protest, not a militant terror attack.

It has become clear that the CIA was aware the attack was distinct from the film protests roiling across other parts of the Muslim world.

Michael Morell rather than David Petraeus now is expected to testify at closed congressional briefings next week on the assault on the consulate in Benghazi, which occurred on the 11th anniversary of the 9/11 attacks.

David Petraeus, who turned 60 on Wednesday, has been married for 38 years to Holly Petraeus, whom he met when he was a cadet at the U.S. Military Academy at West Point, N.Y. She was the daughter of the academy superintendent. They have two children, and their son led an infantry platoon in Afghanistan.

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