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It's interesting to note the subtext in the Petraeus resignation controversy, that the FBI investigation was the result of his paramour "blowing" the affair:

The F.B.I. investigation that led to the sudden resignation of David H. Petraeus as C.I.A. director on Friday began with a complaint several months ago about “harassing” e-mails sent by Paula Broadwell, Mr. Petraeus’s biographer, to another woman who knows both of them, two government officials briefed on the case said Saturday.

When F.B.I. agents following up on the complaint began to examine Ms. Broadwell’s e-mails, they discovered exchanges between her and Mr. Petraeus that revealed that they were having an affair, said several officials who spoke of the investigation on the condition of anonymity. They also discovered that Ms. Broadwell possessed certain classified information, one official said, but apparently concluded that it was probably not Mr. Petraeus who had given it to her and that there had been no major breach of security.

Scott Shane and Eric Schmitt - Biographer’s E-Mails to Woman Led F.B.I. to Petraeus NYT 10 Nov 12

Given Paula Broadwell's biography, "...she specialized in military intelligence, spending time at the U.S. Special Operations Command and the FBI Counterterrorism Task Forces before pursuing an academic career..." according to her publisher, one assumes she knew an email containing classified information would lead to an analysis of her on-line activity and the exposure of her relationship.  Her motivations are further confounded by the unnamed officials' suggestion that "the two women seemed be competing for Mr. Petraeus’s loyalty, if not his affection."  Needless to say her book "jumped from a ranking on Amazon of 76,792 on Friday to 111 by mid-Saturday."
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In another version it is alleged that Ms Broadwell "or someone close to her" had sought access to Petraeus' Gmail account:

Associates of Petraeus had received “anonymous harassing emails” that were then traced to Broadwell, ABC’s Martha Raddatz reported, suggesting she may have found their names or addresses in his e-mail.

Max Fisher - Why David Petraeus’s Gmail account is a national security issue Washington Post 10 Nov 12

Sometimes a cigar is just a cigar but in either scenario Ms Broadwell's activity triggers events leading to the exposure of the relationship and the demise of General Petraeus' otherwise illustrious career.  Another curiosity is the timing, it is clear that the relationship has ended, though it seems it was still ongoing at the time it attracted attention:
The computer investigation began late this spring, according to a person familiar with the investigation. Mr. Petraeus wasn't interviewed by the FBI until recently.

While Mr. Petraeus was still a general, he had email exchanges with the woman, but there wasn't a physical relationship, the person said. The affair began after Mr. Petraeus retired from the Army in August 2011 and ended months ago, the person said.

Devlin Barrett, Siobhan Gorman and Julian E Barnes - CIA Chief Resigns Over Affair WSJ 10 Nov 12

So why are we hearing about it only now?  Specifically just after the presidential election?  Well, that is a puzzle, and it has added fuel to the Right-wing controversy over the Benghazi tragedy as one would expect, given that General Petraeus was scheduled to testify before the Senate Intelligence Committee next week:
According to the New York Times, the Director of National Intelligence James Clapper was only informed about Petraeus's affair at 5pm on election day, and Obama didn't learn of it until Wednesday evening. The timing is just amazing. I am not sure quite what to think.

Booman - Strange Timing of Petraeus Knee-Capping Booman Tribune 10 Nov 11

Interestingly enough, House majority leader Eric Cantor got a tip-off even earlier:
Eric Cantor, the House majority leader, said Saturday an F.B.I. employee whom his staff described as a whistle-blower told him about Mr. Petraeus’s affair and a possible security breach in late October, which was after the investigation had begun.

“I was contacted by an F.B.I. employee concerned that sensitive, classified information may have been compromised and made certain Director Mueller was aware of these serious allegations and the potential risk to our national security,” Mr. Cantor said in a statement.

Scott Shane and Eric Schmitt - Biographer’s E-Mails to Woman Led F.B.I. to Petraeus NYT 10 Nov 12

Curiouser and curiouser; one wonders about the motivations of this "whistle-blower" under the circumstances and their political allegiances in going to the Republican leadership with the story during the election campaign.  It is also interesting to note that while a darling of the Right and an often mentioned presidential prospect General Petraeus was not above suspicion as a source of partisan administration leaks in security matters, coincidentally at just about the time the FBI started their investigation (emphasis added:)
The CIA director had lowered his media profile, stopping his practice of emailing reporters and ending once-common background interviews by the agency. That was especially the case after GOP allegations last spring that the Obama administration was leaking sensitive material to burnish its foreign policy reputation ahead of the presidential election, after a series of stories appeared about top secret operations aimed at al-Qaida in Yemen, and Iran's nuclear program. A White House-ordered investigation of those leaks continues.

Kimberley Dozier and Pete Yost - Official: Emails from paramour led to FBI probe AP via Star-Telegraph 10 Nov 12

Given the controversy over leaks it is worth reviewing the ambivalent reports which have emerged regarding the origin of the FBI investigation in the first instance:
Politico, however, hears that is likely an exaggeration and that concern over access to Petraeus’ e-mail was not what initiated the investigation. McClatchy hears similar information, noting that sources say “the FBI did not investigate the author for attempting to compromise Petraeus’ computer.” According to this version it seems that, as Reuters hears, investigators stumbled across evidence of the affair while investigating news leaks. Although it's unclear exactly why the FBI was monitoring Petraeus’ e-mail, a source tells the Washington Post, the FBI found e-mails describing the affair.

Daniel Politi - How Was Petraeus’ Affair Uncovered and Did he Really Have To Resign? Slate 10 Nov 11

Puzzling, to say the least.  In fact Petraeus had earlier become embroiled in a controversy with neo-conservatives and the pro-Israel lobby with a supposed leaked story in March of 2010, perhaps the nadir of US-Israeli relations:
On Jan. 16...a team of senior military officers from the U.S. Central Command, arrived at the Pentagon to brief Joint Chiefs of Staff Chairman Adm. Michael Mullen on the Israeli-Palestinian conflict. The team had been dispatched by CENTCOM commander Gen. David Petraeus to underline his growing worries at the lack of progress in resolving the issue. The 33-slide, 45-minute PowerPoint briefing stunned Mullen. The briefers reported that there was a growing perception among Arab leaders that the U.S. was incapable of standing up to Israel, that CENTCOM's mostly Arab constituency was losing faith in American promises, that Israeli intransigence on the Israeli-Palestinian conflict was jeopardizing U.S. standing in the region

Mark Perry - The Petraeus briefing: Biden’s embarrassment is not the whole story Foreign Policy 13 Mar 10

This led to an alarmed back-and-forth among neo-conservatives and Petraeus which refuted the detail of the report while substantially confirming the substance and leaving the reader wondering where Mark Perry got the story from in the first instance.  Things got genuinely heated in January 2012 when Perry dropped another intelligence bombshell:
Buried deep in the archives of America's intelligence services are a series of memos, written during the last years of President George W. Bush's administration, that describe how Israeli Mossad officers recruited operatives belonging to the terrorist group Jundallah by passing themselves off as American agents. According to two U.S. intelligence officials, the Israelis, flush with American dollars and toting U.S. passports, posed as CIA officers in recruiting Jundallah operatives -- what is commonly referred to as a "false flag" operation.

Mark Perry - False Flag Foreign Policy 13 Jan 12

Coming as it did at a sensitive time this lit up the neo-conservative pro-Israeli lobby like a skyrocket:
Foreign Policy has produced a slander so outrageous that Israel broke with its strict policy of never confirming or denying covert operations to issue a flat denial – and surprisingly, given Israel’s notoriously poor public relations, it’s a convincing one. On Friday, the magazine published an article by Mark Perry, a military and intelligence analyst who once served as an advisor to Yasser Arafat, that accused Mossad agents of posing as CIA agents to recruit Pakistani terrorists to commit sabotage and assassinations inside Iran. The alleged operation infuriated two successive presidents, George W. Bush and Barack Obama, Perry wrote, because it endangered American lives, undermined America’s relationship with Pakistan and painted America as engaged in terrorist activity. Additionally, Perry said, it convinced many senior American officials that Israel was a liability rather than a strategic asset.

Evelyn Gordon - More About “Foreign Policy’s” Israel Slurs Commentary 16 Jan 12

Serious stuff.  And what was the consensus on the sourcing? (emphasis added:)
The article’s sourcing is problematic and should also raise red flags. Perry relies on two current intelligence officers, only one of whom has seen the memo alleging Israeli malfeasance. One officer—presumably the same who saw the memo and perhaps also wrote it—describes Bush’s reaction, and so presumably was a briefer for the White House. Should Gen. David Petraeus, director of Central Intelligence, wish to identify that leaker, he could do so easily.  [...]

When the intelligence community allows an individual’s political peccadilloes to corrupt its process, it permanently erodes its reputation and ability to conduct its mission. Should Petraeus decline to investigate, there are only three possibilities: He lacks control, he sanctioned the leaks himself, or conversely, his superiors in the White House are willing to corrupt intelligence to sanction anonymous Israel-bashing.

Michael Rubin - Did Israel Run a False Flag Operation? Commentary 16 Jan 12

It is worth noting that one of the above "false flag" pieces also mentions a number of Israeli intelligence scalps which have been taken over the years in similar circumstances:
Israel termed the report “absolute nonsense,” explaining that had it been true, then-Mossad chief Meir Dagan would have been declared persona non grata in Washington rather than being a welcome visitor. Nor is that idle speculation: Those same two presidents forced the ouster of three other senior Israeli defense officials over other issues; why would they have given Dagan a pass?

Just last year, Uzi Arad was forced to resign as chairman of Israel’s National Security Council due to Washington’s anger over leaked information from U.S.-Israeli talks on nuclear issues. And in 2005, two senior Defense Ministry officials – director general Amos Yaron and chief of security Yehiel Horev – were forced out due to Washington’s anger over Israel’s agreement to upgrade Harpy drones for China, following a year in which the Pentagon boycotted Yaron entirely.

Evelyn Gordon - More About “Foreign Policy’s” Israel Slurs Commentary 16 Jan 12

In this geopolitical context it is tempting to imagine a number of motivations for exploring General Petraeus' personal email activity other than the somewhat garbled narrative which has emerged so far regarding a tangential investigation of an erratic lover.  How was it that the internal counter-intelligence watchdogs at the Agency didn't catch this relationship earlier?  And how does the House majority leader get tipped-off about it by an external agency before the president is told?  And what of Ms Broadwell?  We will be watching her career with great interest.

Cross-posted at The Motley Moose and Booman Tribune

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