By all outward appearances, David Petraeus appears to be mounting a comeback. The former general landed a job at powerhouse private-equity firm KKR, has academic perches at Harvard and the University of Southern California and, according to White House sources, was even asked by the President Barack Obama‘s administration for advice on the fight against Islamic State. Yet it turns out that the extramarital affair that forced him to resign as director of the Central Intelligence Agency is still hanging over him.

Most importantly: According to current and former U.S. intelligence officials who have spoken to us, the FBI still has an open investigation into whether Petraeus improperly provided highly classified documents to Paula Broadwell, his biographer and the woman with whom he had an affair.

A little history: In the spring of 2012, the Federal Bureau of Investigation stumbled upon the Petraeus-Broadwell relationship while investigating a separate cyber-stalking matter. While the FBI has cleared Broadwell of those charges, and Obama has said Petraeus never endangered national security, the FBI’s probe remains open.

Two U.S. officials familiar with the investigation say Broadwell was never authorized to receive material that was found on her personal computer. Because this included compartmentalized intelligence that only a handful of very senior officials were approved to view, the FBI considers the breach to be a serious matter. “It was inappropriately shared and it should never have been shared,” one former senior intelligence official said.

Petraeus is not the first senior national security official to be investigated for mishandling classified material. In 1996, CIA director John Deutch was caught with several top secret documents on his home computer. His security clearance was stripped and he pled guilty to a misdemeanor, but eventually was pardoned by President Bill Clinton. Sandy Berger, a Clinton national security adviser, lost his security clearance for three years and paid a $10,000 fine in 2005 for absconding with sensitive documents in his socks from the National Archives.

What stands out here is not just that Petraeus remains under investigation but that he remains under investigation while being reintegrated into the foreign policy establishment.

To wit: Petraeus is ostensibly being investigated for mishandling classified material and yet he retains his security clearance. What’s more, he has been casually advising the White House on Iraq, where he directed the effort to end a civil war in 2007 and 2008 and still maintains close relationships with many of its leaders.

“All of us who know him and are close to him are mystified by the fact there is still this investigation into him,” Jack Keane, a retired four-star U.S. Army General said in an interview. Keane has been both an adviser to and mentor of Petraeus since he saved Petraeus‘s life during a live-fire training exercise in 1991.

Keane questions whether the Petraeus FBI probe lasting this long may be driven by something other than a desire to investigate a potential crime. “It makes you wonder if there is another motivation to drag an investigation out this long,” he said.

He is not alone. “This is not a case where you are leaking classified information to the press or providing information to America’s enemies,” said Pete Hoekstra, who served as the Republican chairman of the House Permanent Select Committee on Intelligence between 2004 and 2007. “You have people in this case who are willing participants in the investigation. Having that thing still hanging out there two years later is rather surprising.”

As reported by Fox News last summer, Representative Jason Chaffetz (now the incoming chairman of the House Committee on Oversight and Government Reform) had previously asked the Justice Department for answers on why the Petraeus file might still be open. “If he has done something wrong, charge him, if he has not, let him go,” Chaffetz told us last month. “At this point I don’t know what their motivation is. But I worry they will let this linger until the president leaves office.”

A Justice Department spokesman declined to comment for this article: “We refer you to past comments on the matter and have nothing to add.” The latest public comment on the investigation was from April 8, from Attorney General Eric Holder in response to a query from Chaffetz at a hearing of the House Judiciary Committee. Holder said: “All I can say is that this is an ongoing investigation. I’m really not in a position to say much more about it than that.” (Lawyers for Petraeus and Broadwell also declined to comment.)

Petraeus allies both inside and outside the U.S. intelligence community and the military express a concern that goes beyond a criminal probe: that the investigation has caused Petraeus to trim his sails ― that one of the most informed and experienced voices on combating terrorism and Islamic extremism is afraid to say what he really thinks, a sharp juxtaposition to Bob Gates and Leon Panetta, two former defense secretaries who have not been shy about criticizing Obama‘s national security team.

Between his resignation as CIA director in November 2012 and June of this year, Petraeus largely stayed out of the public debate over foreign policy. When he did enter the fray, it was in careful statements to the press that have been friendly to Obama. For example, in September 2013, he urged Congress to support a White House resolution to strike Syria.

Petraeus has also publicly supported Obama’s handling of the new crisis in Iraq and Syria. On June 18, when pressure in Washington and the Middle East was mounting for Obama to strike IS targets in Syria and Iraq, Petraeus hewed closely to the White House line, warning that any support for Iraq should be conditioned on a new, more inclusive government being formed in Baghdad.

On one level, this lack of outspokenness is not surprising. Petraeus is still rehabilitating his public image, and he may feel he is getting his point across in his private communications with the White House. But what does seem surprising, to many who know and have worked with him, is that the views he has been expressing are so at odds with what he has said and implied in the past.

For example, when Petraeus was inside Obama’s administration in his first term, he advocated for more troops inside Afghanistan and made the case for arming Syrian moderate forces. But when asked this summer about that effort, Petraeus demurred and focused on Obama’s new $500 million initiative in 2014 to train Syrian rebels. “I strongly support what’s being done now,” he said. “Half a billion dollars is a substantial amount of resourcing to train and equip.”

Petraeus’s rhetoric on Iraq and Syria differs sharply not only from his past positions, but from that of many retired generals of his generation and of his biggest supporters.

At a Sept. 18 hearing before the House Intelligence Committee, retired General James Mattis, who took over the U.S. Military’s Central Command from Petraeus in 2010, was very critical of Obama’s decision to say ahead of time that no U.S. combat forces would be deployed to Iraq. “We have the most skillful, the fiercest and certainly the most ethical ground forces in the world,” he said. “And I don’t think we should reassure the enemy in advance that they will never face them.”

Chaffetz says that the fact that Petraeus hasn’t publicly criticized the White House on Iraq may not be an accident. “When the president has the ability to charge him with crimes, maybe it affects your perspective,” Chaffetz said. “I don’t know.” 

By Eli Lake and Josh Rogin

Eli Lake and Josh Rogin are Bloomberg View columnists who write about foreign affairs. ― Ed.

(Bloomberg)