The Defense Department’s inspector general has found that allegations that Gen. John Allen engaged in inappropriate behavior in emails he exchanged with Tampa, Fla., socialite Jill Kelley were unsubstantiated. 

"The IG cleared him," a defense official told NBC News, speaking on condition of anonymity. 

Allen, the current commander of NATO forces in Afghanistan, has been nominated to be Supreme Allied Commander in Europe, but that promotion was put on hold when the IG investigation began. The defense official stressed that no decision has been made yet on whether his nomination will go forward again. 

A statement Wednesday by the International Security Assistance Force in Afghanistan on behalf of Allen said he had been informed that investigators  “the allegations against him were unsubstantiated and … that he did not violate the requirement of exemplary conduct or the prohibition against conduct unbecoming an officer and a gentleman. “

“He's obviously pleased by the outcome,” it said. “But more critically, he is grateful for the support he received throughout this process from his chain of command, friends, family and colleagues.  He remains focused, as he has always been, on leading the brave men and women of the ISAF team."

Allen’s nomination was jeopardized  in mid-November when it was revealed that he had exchanged emails with Kelley that some Pentagon officials at the time characterized as “inappropriate” and “flirtatious.” 

Allen had met Kelley when he was commander of MacDill Air Force Base outside Tampa, where she served as a volunteer “social liaison.” 

She inadvertently drew him into the scandal that led to the resignation of former CIA Director David Petraeus by complaining to an FBI agent with whom she was acquainted about anonymous emails referencing Petraeus. Among those emails was one that Allen had forwarded to her in the belief that she had sent it to him as a joke, officials told NBC News at the time. 

FBI agents eventually traced the allegedly threatening emails to Paula Broadwell, Petraeus' biographer. That investigation also led to evidence of an extramarital affair between Petraeus and Broadwell, prompting his resignation on Nov. 7. Days later, Defense Secretary Leon Panetta announced the investigation into Allen’s relationship with Kelley. 

Jill Kelley speaks out: 'I knew I was being stalked'

The inspector general’s investigation does not determine guilt or innocence. Rather, it decides whether an allegation is substantiated or not. Even if the finding is that the allegation is unsubstantiated, the IG can still make a recommendation that can harm an officer’s career. 

Jim Miklaszewski is NBC News' Chief Pentagon Correspondent; Courtney Kube is an NBC News producer at the Pentagon. Mike Brunker, NBC News investigations editor, contributed to this report.

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Ethan Miller / Getty Images file

Radio talk show host Bubba the Love Sponge, the performing name used by Todd Alan Clem, is shown attending the Adult Video News Awards Show on Jan. 12, 2008, in Las Vegas.

When a Florida shock jock threatened to "deep fat fry" a Quran earlier this year, Gen. John Allen, the commander of U.S. and NATO troops in Afghanistan, and CIA Director David Petraeus both reached out to Tampa socialite Jill Kelley to help tamp down what they saw as a potential threat to the safety of U.S. troops, according to emails released by the city of Tampa.

In the emails, Kelley -- indicating she was acting at the behest of the high level U.S. government officials -- asked Tampa Mayor Bob Buckhorn to intervene and get the radio disc jockey to stand down.

"I have Petraeus & Allen both emailing me about getting this dealt with," Kelley wrote to Buckhorn in a March 7 email. The day before, Kelley mentioned similar requests to Buckhorn from both Allen and Vice Adm. Robert Harward, deputy commander of the U.S. Central Command in Tampa. "I just got off the phone with Gen. Allen & Adm Harward," she wrote. "I'm going to need your assistance, vice versa with the potential crises we'll be dealing with."

The emails offer a new glimpse at Kelley's relations with top  U.S. military officials -- as well as Petraeus, who had by then left the military to take the helm at the CIA -- shortly before she went to an FBI agent to complain about anonymous harassing emails she was receiving. The resulting FBI probe into what was initially viewed as a potential case of "cyber-stalking" led to Petraeus’ resignation as CIA director and triggered a separate investigation by the Pentagon inspector general into what has been described as "potentially inappropriate" email correspondence between Allen and Kelley.

Numerous government and law enforcement officials have told NBC News that the FBI investigation revealed that Petraeus' biographer, Paula Broadwell, had sent the threatening emails and that agents subsequently uncovered evidence that she had an extramarital affair with Petraeus.

Newer emails to Buckhorn also show Kelley's anxiety as the scandal broke last week and the media descended on her home.

/

Jill Kelley leaves her Tampa, Fla., home on Tuesday.

"Can you help out with obstruction by the paparazzi, since they're blocking our driveway, and continue to trespass on my property," she wrote Buckhorn on Tuesday. "My kids are scared and need their 'home' back."

In other emails to Buckhorn, Kelley referred to numerous social events with generals from Central Command – and referred repeatedly to Petraeus and others. One also described a post-election visit to the White House, just before the scandal broke.

"ps I'll be in DC this weekend with Petraeus, but let's set up a double date when I return!" she wrote to Buckhorn on Oct. 9, 2011. The next day, she added, "I'll be sure to send the Director your regards --should be another fabulous weekend in DC."

On Nov. 24, 2011, she wrote: "We just got back from spending the weekend with the Petraeus (it was Dave's 59th Birthday) and he said to send you his best! :) "

On Jan. 13 of this year, she wrote to an aide to Buckhorn: “I’m up in DC having dinner tonight with Gen. Petraeus and Gen. John Allen (he replaced Petraeus as the Commander in Afghanistan.)”

The email correspondence included an effusive account of a dinner with the king of Jordan, Abdullah II bin Al-Hussein. “The King and his sister (the Princess) are awesome people!” Kelley wrote to the mayor on May 16, 2011.

Kelley also sent a formal invitation to a party in her honor at the U.S. Central Command  on April 19 -- forwarded by Centcom's chief of protocol.

 "Vice Admiral Robert S. Harward, Deputy Commander, United States Central Command request the pleasure of your company at a ceremony in honor of Mrs. Jill Kelley," the invitation reads in part.

 A military source said the party honoring Kelley was to formally give her the title of "Honorary Ambassador to the Coalition" -- a certificate given to private citizens who are "friends" of the base. Kelley used the title in her later email correspondence: "Today, I will be hosting a group of VIPs visiting from Afghanistan Pakistan Nepal, here by the authority of the State Department," she wrote Buckhorn on May 14. "As the Ambassador to the Coalition, I will taking them to Centcom with the great assistance of Gen. Mattis & Adm Harward." (Marine Gen. James Mattis is the commander of U.S. Central Command at MacDill Air Force Base.)

Broadwell, Kelley both were repeat White House visitors, official says

Kelley’s access to the military elite continued right up to this month. On Nov. 8 — just a day before Petraeus resigned as CIA director -- she emailed Buckhorn: “I was at the WH with my friends in the Administration this weekend—the stress was surreal! But glad POTUS has been re-elected!”

Kelley's emails referring to the comments about burning the Quran by the Tampa shock jock, known as "Bubba the Love Sponge Clem," reflected a genuine concern among U.S. military officials that they would endanger U.S. troops, a U.S. military official told NBC News. At the time, there were riots and deaths in Afghanistan over the burning of Qurans by U.S. soldiers.

 "It was absolutely a concern," Lt. Col. T.G. Taylor, CentCom spokesman, said in an interview. Taylor said he personally called the disc jockey and told him, "Look Bubba, somebody's going to get hurt if you do this." He was "completely reasonable and said he understood," Taylor added.

Buckhorn, the Tampa mayor, told Kelley when she emailed about the issue that the city's police chief was handling the matter, but added: "This Bubba the Love Sponge is a complete moron." 

For his part, the disc jockey told the Tampa Bay Times that he abandoned his plans to “deep fat fry” a copy of the Quran, the Muslim holy book, at the request of local law enforcement and credited Kelley’s role: “Probably she did get Intel to have me stop it, and that’s the problem itself,” he said. 

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James Brantley

Multiple sources tell NBC News the woman with her back to the camera in the top photo is Paula Broadwell. She is pictured at a reception prior to the annual OSS Society awards dinner in Washington on Oct. 27, speaking to a man who is nearly obscured in the photo. The photographer and a senior U.S. intelligence official tell NBC News that the man is Gen. David Petraeus, also attended the event. The photo below, taken approximately a minute later, shows Petraeus speaking to one of the unidentified guests in the first photo.

Two weeks before his resignation as CIA Director, David Petraeus and his biographer, Paula Broadwell, met at an event honoring one of Petraeus' predecessors, NBC News has learned. It is the last known meeting between the two before the scandal that cost Petraeus his job went public and occurred after Broadwell had admitted to the FBI the two had an extramarital affair, according to multiple government and law enforcement officials. 

One senior U.S. intelligence official who attended the event – the annual Office of Strategic Services Society awards dinner -- tells NBC News that he saw the two speak to each other at the Oct. 27 event. The official did not know details of the conversation.

And photographer James Brantley, who worked the event, said he is certain the two spoke, based on the photos above, which he estimated were taken about a minute apart. The first shows Broadwell speaking to a man who is nearly obscured in the photo, as two unidentified guests look on. The second, taken from a different position, clearly shows Petraeus speaking to one of the other guests from the first photo.

The duo’s presence at the same event was first reported by the conservative weekly Human Events, which said they attended together. But numerous partygoers interviewed by NBC News disputed that.

Still, their public proximity raised eyebrows after the events of last week unfolded.

Said one former senior U.S. intelligence official who attended, “It’s mind-boggling that she could be so reckless as to show up at high-profile events like this, shortly after learning the FBI was investigating their affair.” 

Charles T. Plinck, director of the OSS Society, did not return phone calls seeking comment from NBC News.

Email to Gen. Allen among those Kelley gave to FBI

The event came more than a month after Broadwell was first interviewed by the FBI following discovery of compromising emails that ultimately led to Petraeus' resignation on Nov. 9.  Days after the event, the FBI would interview Petraeus for the first time and Broadwell for a second time. The event also occurred about four months after the two reportedly broke off their 10-month affair.

Slideshow: Petraeus case: Cast of characters

ISAF via Reuters file

Meet the people who have been pulled into the scandal that caused Gen. David Petraeus to resign.

Launch slideshow

The dinner is the annual award ceremony of the OSS Society, a group dedicated to honoring veterans of the Office of Strategic Services, the World War II predecessor to the Central Intelligence Agency. Petraeus, who sources described as being in a "great mood" that night, gave one of the speeches honoring former CIA director and Secretary of Defense Robert Gates, the recipient of this year's William Donovan Award, named for the director of the OSS.

The dinner is one of the intelligence community's most high-profile events. It attracts top U.S. and international intelligence officials, former directors of the CIA and other U.S. intelligence agencies.  In addition to Petraeus and Gates, others who attended included John Bennett, director of the CIA’s National Clandestine Service; William Webster, former head of both the CIA and FBI; Adm. Mike Mullen, former chairman of the Joint Chiefs of Staff, and Ambassador Hugh Montgomery, former director of the State Department's Bureau of Intelligence and Research.

Robert Windrem is a senior investigative producer with NBC News.

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