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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At least one anonymous email sent to Gen. John Allen, commander of U.S. and NATO forces in Afghanistan, was among those turned over by Tampa, Fla., socialite Jill Kelley to the FBI in June, a senior law enforcement official and a source close to Kelley tell NBC News. Kelley’s complaint to an FBI agent with whom she was acquainted triggered the investigation that ultimately led to the resignation of CIA Director David Petraeus.

The law enforcement official, who spoke on condition of anonymity, said Wednesday that Kelley turned over fewer than a dozen emails to the FBI agent, including at least one that Allen had received and forwarded to her.  The emails were ultimately traced to Paula Broadwell, Petraeus’ biographer and the woman with whom he had an extramarital affair, multiple government and law enforcement officials have told NBC News.

The official said it is not clear who received email from Broadwell first -- Kelley or Allen – but a person close to Kelley told NBC News on Wednesday that Allen received the first email in mid-May. According to the source, who also spoke on condition of anonymity, the email sent from an account called "kellypatrol" said , in essence, “Beware of Jill Kelley. She's the kind of person who could ruin you.” It also referred to a meeting Kelley and her husband were planning in Washington with Allen, the source said.

Allen forwarded the e-mail to Kelley, thinking it was a joke from her. She replied that she hadn’t sent it, the source said.

The law enforcement official said Allen also forwarded the email to a “military authority” within the Department of Defense. The official did not specify which office or individual was notified.

Kelley herself began receiving similar emails in early June, the source close to her said, sent from four or five alias accounts. They contained words to the effect of, “What kind of person are you.” And passages directed to her husband, asked, in essence, “Do you know what your wife is up to?” the source said.

As reported previously by NBC News, Kelley took the emails – including at least one from Allen – to the FBI agent she knew because they made reference to meetings she had planned with both Allen and Petraeus, the source said. Kelley wondered why an anonymous e-mailer would know that kind of detail and became concerned that someone was cyberstalking her or hacking into her e-mails, the person said.

Federal officials confirmed Wednesday that the agent who first took the complaint from Kelley is Frederick Humphries, a counter-terrorism agent who worked on the millennium bomb plot case. His name was first revealed by the New York Times.

-- / AFP - Getty Images

Tampa, Fla., socialite Jill Kelley, left, inadvertently triggered the FBI investigation of CIA Director David Petraeus by turning over anonymous threatening emails -- including one sent to Gen. John Allen -- to the FBI.

A senior defense official, also speaking on condition of anonymity, confirmed that Allen had received an anonymous email “some time ago” warning him to be careful around Kelley. The official, who had not seen the email but was generally familiar with its contents, said the general forwarded it to “proper authorities” within the military.

“He did the right thing,” the official said.

The defense official confirmed that the email also was forwarded to Kelley and her husband, Scott, but said it was not certain that Allen was the one who sent it to them. Allen did send Kelley an email referencing the anonymous note he had received, the official said.

The source close to Kelley and several law enforcement officials tell NBC News that Broadwell used multiple anonymous accounts to send the emails to Kelley and Allen. She “covered her tracks” by sending them from cybercafés, the source said.

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

Meanwhile, defense officials tell NBC News that while there is no evidence that Allen and Jill Kelley engaged in an extramarital affair, there was enough “inappropriate” language in emails they exchanged to warrant an investigation by the Pentagon’s inspector general.

According to one official, who like the others spoke on condition of anonymity, a small number of emails contained language that could be considered “inappropriate” or even “suggestive.” 

But even without those, an investigation of the email correspondence between Allen and Kelley was inevitable given the circumstances, the officials said.

“We had no idea what was going on,” one said. “The last thing we want is to be accused of a cover-up,” regarding the Allen emails. 

Courtney Kube and Mike Brunker of NBC News contributed to this report.

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A June 23, 2011, file photo shows Paula Broadwell, second from left, watching as Gen. David Petraeus and his wife, Holly Petraeus arrive for a Senate Select Intelligence Committee hearing on Petraeus' nomination to be director of the Central Intelligence Agency.

What began with David Petraeus’ surprise resignation as CIA director on Friday resulting from an extramarital affair has now spiraled into a complicated story of infidelity, intrigue and politics.

Petraeus’ admission of an extramarital affair quickly led to his biographer, Paula Broadwell, and an examination of her relationship with the decorated war hero. The length of the FBI’s investigation of “menacing” emails sent to Petraeus’ family friend Jill Kelley, and the timing of the announcement of his departure from the Obama administration fueled conspiracy theories. Then Gen. John Allen, Petraeus’ successor as military commander in Afghanistan, was embroiled in the scandal, accused by U.S. officials of sending “inappropriate” emails to Kelley.

To help you keep the facts straight, NBC News has compiled this timeline, based on reporting by NBC News and other published accounts:

Spring 2006 -- Paula Broadwell meets Gen. David Petraeus, when she introduces herself after he gave a speech at Harvard's Kennedy School, where Broadwell was working on a master's degree, the Wall Street Journal reported. 

October 2008 -- Petraeus takes over as head of U.S. Central Command, based at MacDill Air Force Base. While serving there, he reportedly meets Jill Kelley and her husband, Dr. Scott Kelley. She is described in various accounts as a volunteer “social liaison” between the community and the base.

2008 -- Broadwell begins her doctoral dissertation, "a case study of General Petraeus’ leadership," according to Rolling Stone magazine.  

June 2009 -- Broadwell and her husband, Scott, purchase a home in Charlotte, N.C., the Charlotte Observer reports. 

June 2010 -- Petraeus is named as replacement for Gen. Stanley McChrystal as the top commander in Afghanistan after the latter makes impolitic remarks to a Rolling Stone reporter. Broadwell decides to turn her dissertation into a book.  

July 2010-July 2011 – According to an online biography of Broadwell that was taken down after Petraeus’ resignation, she made multiple trips to Afghanistan during this period, where she “embedded with the general, his headquarters staff and his soldiers on the front lines of fighting across Afghanistan to chronicle the experiences of this American general as they are brought to bear in the terrible crucible of war.”  

Aug. 31, 2011 -- Petraeus retires from the U.S. Army, departs Afghanistan.

Sept. 6, 2011 -- Petraeus takes over as director of the CIA.

Early November 2011 – According to former Petraeus spokesman Steve Boylan, who had spoken to his former boss after his resignation, Petraeus' affair with  Broadwell began around this time, approximately two months after he took the CIA job.  

January 2012 – “All In, The Education of General David Petraeus,” by Paula Broadwell with Vernon Loeb is published by Penguin Press.

May 2012 – “Menacing” emails – five to 10 of them, according to the Wall Street Journal -- began arriving in Jill Kelley's inbox, NBC’s Michael Isikoff and Pete Williams report. 

Emails on 'comings and goings' of Petraeus, other military officials escalated FBI concerns

June 2012 – The FBI investigation begins. A source close to Kelley tells Isikoff that she took the emails, which she viewed as harassing or menacing, to the FBI. The source said the anonymous emails didn’t mention Petraeus by name, but subsequent emails – sent from multiple alias accounts -- contained references to the "comings and goings" of high-level military officials -- including events that were not on any public schedule. This raised the question as to whether somebody had access to sensitive -- and classified -- information about the CIA director. 

T.Ortega Gaines / Charlotte Observer via Reuters

Paula Broadwell is pictured before embarking on a national book tour to promote "All In," her biography of Gen. David Petraeus.

July 2012 – Approximate end of the affair between Broadwell and Petraeus, according to former Petraeus spokesman Steve Boylan, who  tells NBC’s Kristen Welker in early November that it ended “about four months ago.” 

Late  summer -- Attorney General Eric Holder is told that agents have discovered an email link between Petraeus and Broadwell, which included exchange of “explicit details of a sexual nature,” according to the Wall Street Journal. 

September – FBI agents interview Paula Broadwell for first time, NBC’s Pete Williams reports.

Oct. 27  -- House Majority Leader Eric Cantor speaks to an FBI agent who had worked on the Petraeus investigation, according to Cantor spokesman Doug Heye. The agent-- who had originally contacted Rep. Dave Reichert, a Republican from Washington -- raised concerns that "sensitive information" relating to Petraeus may have been "compromised," Heye said. The timing of the tip to Reichert is not clear.

Week of Oct. 29 – FBI agents interview Petraeus and Broadwell (for a second time), according to NBC’s Michael Isikoff.

Approximately Oct. 30-31 – Somewhere around this time frame, Petraeus traveled to Tripoli to conduct his own personal inquiry into Benghazi, according to author Bob Woodward, appearing on "Meet the Press" on Nov. 11. NBC’s Andrea Mitchell confirmed that Petraeus had recently traveled to Libya.

Oct. 31 – After conferring with his chief of staff, Steve Stombres, and Richard Cullen, a former attorney general of Virginia, Cantor had Stombres call the FBI chief of staff to relay the information he had received from the FBI agent, NBC News has reported.

Nov. 1 -- Cantor aide Steve Stombres is told by the FBI that it cannot confirm or deny an investigation, but the bureau official assured the leader's office it was acting to protect national security.

Nov. 2 – The FBI concludes its investigation, according to NBC News’ Michael Isikoff, citing senior U.S. law enforcement official; the  last FBI interviews with both Broadwell and Petraeus also took place this day, NBC’s  Pete Williams reports, citing federal officials.

Nov. 6 – Justice Department informs Director of National Intelligence James Clapper.

Nov. 7 – Clapper informs the White House.

Nov. 8 –  Petraeus calls White House Deputy Chief of Staff Thomas Donilon and asks to see the president, NBC’s Andrea Mitchell reports. The White House tells Obama of the FBI investigation of Petraeus and his admission of an extramarital affair.

Nov. 9 – Obama accepts Petraeus’ resignation; Senate and House leaders first learn of it from media calls. They then speak to Petraeus, but don’t hear directly from the president, Mitchell reported.

Nov. 11 – Jill Kelley and her husband, Scott, issue statement: "We and our family have been friends with Gen. Petraeus and his family for over five years. We respect his and his family's privacy and want the same for us and our three children."

Afghanistan military commander Gen. John Allen investigated for 'inappropriate' emails

Chuck Burton / AP

FBI agents carry boxes and a computer from the home of Paula Broadwell in Charlotte, N.C.

Nov. 12 – In a surprise statement during a trip to Australia, Defense Secretary Leon Panetta announces that U.S. General John Allen, who succeeded Petraeus as military commander in Afghanistan, is under investigation over allegations he exchanged “inappropriate” emails with Kelley, the woman who triggered the investigation of Petraeus. Meanwhile, FBI agents carry out a four-hour “consensual search” of Broadwell’s home in Charlotte, N.C., leaving with eight to 10 cardboard boxes.

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New in this version: FBI search Paula Broadwell's home Monday night; officials say the FBI agent who worked with Jill Kelley, the Tampa, Fla. woman who received anonymous emails from Broadwell, was dismissed from case because he became obsessed with Kelley.

Updated at 11:36 p.m. ET: “Menacing” anonymous emails that launched the FBI investigation which ultimately brought down CIA Director David Petraeus contained references to the “comings and goings” of high-level U.S. military officials, raising concerns that someone had improperly gained access to sensitive and classified information, a source close to the recipient tells NBC News.

The first email sent anonymously to Jill Kelley, the Tampa, Fla., woman who reported the threatening emails to the FBI, in May referred to Kelley socializing with other generals in the Tampa area and suggested it was inappropriate and should stop, according to the source close to Kelley, who spoke with NBC News on condition of anonymity.

After Kelley alerted the FBI, agents began pursuing it as a possible case of cyber harassment or stalking. "The thought was she was being followed," the source said.

The anonymous emails continued -- sent from multiple alias accounts -- and some later ones in the sequence contained references to Petraeus, though not by name, the source said.

What most alarmed Kelley and the FBI, the source said, were references to "the comings and goings" of high-level generals from the U.S. Central Command, which is based at MacDill Air Force Base in Tampa, and the U.S. Southern Command, as well as Petraeus -- including events that were not on any public schedule. This raised the question as to whether somebody had access to sensitive -- and classified -- information.

Moreover, the sender of the emails had "covered her tracks pretty well," the source said.

Multiple government and law enforcement officials have told NBC News that FBI agents traced the emails to Paula Broadwell, Petraeus’ biographer. In the course of the investigation, the agents also discovered emails between Petraeus and Broadwell that were indicative of an extramarital affair, they said.

The source close to Kelley said that she had never met Broadwell and had no idea who she was. The source also stressed that Kelley has been active in multiple social events in the Tampa area and is purely a social friend of the Petraeus family.

Meanwhile, it has come to light that the FBI agent contacted by Kelley about the emails she received from Broadwell was removed from the case. According to officials, the agent’s supervisors said he had become infatuated with Kelley and had sent her shirtless photos of himself.

The FBI remains involved in the case, however. On Monday evening, plain-clothed FBI agents arrived at Broadwell’s home in Dilworth, N.C. around 9 p.m. Monday night for what a senior law enforcement official called a “consensual search.” The official said the search is not a raid and “not a game changer.”

Rather, the official said that the FBI is being thorough as it finishes its investigation into Broadwell and whether she violated cyber-stalking or cyber-bullying laws.

The investigation of Petraeus has concluded. Law enforcement sources tell NBC News that Petraeus is not under investigation and that they don't expect their inquiry will result in criminal charges.

The search of Broadwell's home is not expected to yield information that would lead to charges against her, the official said. At the house, agents did not respond when reporters asked for their affiliation, although WCNC in Charlotte, N.C. confirmed they were with the FBI.

NBC News has been unable to reach Broadwell for comment.

The new information offers clues about how federal investigators could connect a handful of anonymous emails to Broadwell, a trained intelligence officer who spent years working with some of the most secretive agencies in the world.

Federal officials who spoke with NBC News on condition of anonymity on Monday said it took agents a while to figure out the source. They did that by finding out where the messages were sent from -- which cities, which Wi-Fi locations in hotels. That gave them names, which they then checked against guest lists from other cities and hotels, looking for common names. 

That led them to Broadwell, they said, noting that the pattern coincided with her travel to promote her book.

Finding the location from which the emails emanated would not have been difficult, experts say.

Some webmail services, including Yahoo and Microsoft's Outlook.com, send user IP addresses across the Web with every note, according to privacy researcher Chris Soghoian, a senior policy analyst at the American Civil Liberties Union. Those IP addresses can be used to track the physical location of a computer user connected to the Internet, sometimes without the help of an Internet service provider.

Broadwell had used a Yahoo account publicly in the past. If she used a new, fake Yahoo account for some of those anonymous emails, agents would have had an easy time gathering a list of IP addresses from the threatening emails Kelley provided to them. And even if she had used Gmail or another service that doesn't "leak" IP information, an FBI agent could have obtained such information by calling Google with a subpoena, the experts said.

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

Once there was evidence to link Broadwell to the emails, agents would have had little trouble proving probable cause and getting a warrant under the provisions of the Stored Communications Act, which would allow them to access any emails sent or received during the prior 180 days. Agents could also have sought a wiretap order and monitored Broadwell’s email in real time, though wiretaps are more challenging to obtain, and there is no indication that agents took that step.

Soghoian said the successful cyberhunt for Broadwell shows anonymity is much harder to preserve than many Internet users realize.

"We see this again and again. We saw it with the Anonymous (hacker) arrests last year.  The lesson for the rest of us here us you have to go through a lot of steps to maintain anonymity, and you only have to screw up once," said Soghoian. "The FBI was able to pierce the veil of anonymity even for someone who's been trained. The government only has to get one clue. You have to be successful 100 percent of the time (when trying to hide)."

NBC News Justice correspondent Pete Williams contributed to this report.

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After investigating a potential case of "cyber-harassment" for several months, the FBI wrapped up its case after interviewing Paula Broadwell -- the biographer of former CIA director David Petraeus -- on Friday, Nov. 2, four days before the presidential election, a senior U.S. law enforcement official told NBC News.

It was the second time that FBI agents had questioned Broadwell in the probe and during both interviews she acknowledged having had an affair with Petraeus, the official said. Petraeus himself had been questioned a few days earlier and also acknowledged the affair, the first official said.

The dual interviews the week of Oct. 29 -- among the last to be conducted by the FBI in the case -- allowed the FBI to formally conclude there was no basis for criminal charges in the matter. This explains why the Director of National Intelligence James Clapper wasn't told about the probe until the following Tuesday, Nov. 6, election day, the official said.

The official offered new details about the FBI investigation -- and a more precise timeline of key events-- in order to rebut suggestions that senior law enforcement officials held back key information about the Petraeus matter until after the election.

The FBI and Justice Department's decisions on the case were not governed by the political calendar, the official asserted. Nor, the official said, were they influenced by a phone call from House Majority Leader Eric Cantor's office to the FBI on Oct. 31 asserting that it had heard from a FBI whistleblower who raised concerns that the Petraeus matter was being covered up or not being taken seriously.

Lawmakers question timing of Petraeus resignation

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

According to reporting by NBC’s chief justice correspondent Pete Williams, a senior law enforcement official said a call to a congressional staffer came from an agent who was initially involved in the investigation but who was later removed from the case because he knew an associate of one of the people being investigated.  The agent knew someone on the Hill and called that person, a Republican staffer, according to the official. But that phone call had no effect on either the course of the investigation, the involvement of Mueller -- who was following it closely long before Cantor called him -- or the decision to notify Clapper, the official says.

"This had nothing to do with the election," the official said. Moreover the official added, Cantor's office was told that the case was being actively investigated by the FBI when it raised the matter on Oct. 31, and so it would have been wrong for the FBI or Justice Department to inform higher level officials in the administration about the probe earlier -- because they were unsure at that point what they were dealing with. In the end, according to multiple officials, investigators determined there was no criminal wrongdoing.

According to the senior official, the investigation began several months ago when a woman reported to the FBI she had received anonymous-- and harassing -- emails from a person she didn't know. Multiple government officials tell NBC News that the woman was Jill Kelley, who lives in Tampa, Florida. Kelley and her husband, officials say, are close friends of the Petraeus family. Kelley was a volunteer social liaison to the MacDill Air Force Base in Tampa.

The FBI viewed the matter as a potential case of "cyber-harassment" and it was handled "regionally" with federal prosecutors working with the FBI on the matter, the official said. At first, neither Kelley nor the FBI knew who was sending the harassing emails-- because they came from accounts that were not immediately identifiable. But the FBI was eventually able to determine they came from Broadwell and then obtained access to her regular email account. It was only then that the FBI discovered, through her email exchanges with Petraeus, an apparent relationship between the two of them, the official said.

The FBI continued investigating the matter and was close to wrapping up the case late in October, the official said. Agents finally interviewed Petraeus the week of Oct. 29 and then re-interviewed Broadwell, allowing them to complete their investigation, according to multiple officials. It was only at that point that the decision was made to pass along information about the case to Clapper, the senior law enforcement official said, setting in motion the chain of events that led to Petraeus' resignation.

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NBC's Kristen Welker contributed to this report.