David Petraeus’ affair with his biographer ended his 37-year career. But the damage from this episode goes far wider

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Karen Bleier / AFP / Getty Images

CIA Director David Petraeus testifies before the U.S. Senate Intelligence Committee during a full committee hearing on "World Wide Threats" in Washington, D.C. Jan. 31, 2012

Paula Broadwell stepped off the stage at the Aspen Security Forum on July 28, fresh from criticizing the news media for heedless disclosure of secrets. The afternoon program of seminars was packed with admirals, generals and Cabinet chiefs, but Broadwell had pressing business elsewhere. She ducked out of the conference, slipped into running shorts and jogged off in search of a once-in-a-­lifetime birthday present.

Broadwell and CIA Director David Petraeus had fallen into an extramarital affair after years of close contact as biographer and subject. Born two days and 20 years apart, they had big benchmarks approaching—his 60th, her 40th—and Broadwell was looking for a suitably momentous gift. As she had tweeted proudly a few days before, Broadwell had a date for a “1v1 run with Lance Armstrong.” What she did not mention was her plan to recruit Armstrong for a surprise birthday bike ride with the fitness-mad Petraeus. If all went as she planned, the retired four-star general would ride into his seventh decade alongside cycling’s greatest star.

(LIST: Who’s Who in the David Petraeus ‘Love Pentagon’ Scandal)

That particular ride was not to be. By then, though they did not know it yet, disgrace was bearing down on all three of them. Tampa socialite Jill Kelley, alarmed by a series of disturbing e-mails from someone self-identifying as “kelley­patrol,” had filed an FBI complaint in May. Electronic metadata pinpointing the times and places and IP addresses associated with Kelley’s hidden correspondent identified Broadwell as the author. Investigators scooped up gigabytes of content from her other accounts—some under Broadwell’s name, others under aliases. As FBI agents sifted through the harassing e-mails, they found discussion of the movements and activities of high-level military officials—and of Petraeus. “So that sparked the interest of the investigative agencies,” says a law-enforcement official. Some of the exchanges were sexually charged. By that point the implications extended far past a domestic dispute into the highest reaches of national security.

Photograph by Marco Grob for TIME

Already the costs have been stunning. Marriages and reputations have been fractured. Multiple careers, including those of the CIA director and a four-star general, have been damaged or destroyed. The decision by FBI Director Robert Mueller and Attorney General Eric Holder Jr. to withhold notice about the case until Election Day has turned congressional attention once again on the inner workings of the Obama Administration. Intelligence Committee members in Congress are furious at having been kept in the dark, and the furor has strained relations between lawmakers and the White House at the very moment voters want to see them sit down together to get something done. The U.S.’s entire security apparatus seems rattled. And every news cycle brings new questions about the judgment, morals, methods and command focus of some of America’s most powerful public servants.

Obama lost his CIA director just as the rest of his national-security team was in motion as well: Hillary Clinton is preparing to leave the State Department, and replacing her is likely to involve further shuffling of key players. And this was not just any CIA director but a man with long experience of command in the Middle East and South Asia, at a moment of intense focus on Libya, Syria and the looming pullout from Afghanistan. Obama was also losing one of the most experienced operators of and thinkers on lethal drones for targeted killing, the President’s chosen tool against al-Qaeda. And all this comes as complex problems in Iran and China await Obama’s attention. A President who had hoped to pivot to a second term of bipartisan purpose found himself dodging questions about how his team had handled the far-reaching implications of a love affair.

(MORE: Jill Kelley: Military Liaison and Whistleblower in Petraeus Scandal)

“The Party Is Canceled”
For Petraeus, there would be no birthday celebration. On Nov. 7, the day he turned 60, he was preparing for his meeting with Obama the following afternoon, when he would tender his resignation. Two days later, when Broadwell turned 40, Petraeus publicly announced that he was stepping down after “engaging in an extramarital affair.” Broadwell was at a birthday dinner with her husband at the Inn at Little Washington in Virginia on the night news reports identified her as the woman involved. A hasty e-mail that evening from her husband to guests invited for a larger celebration said simply, “The party is canceled on Saturday. Thanks!”

Yet that was just the beginning. Friends and family said Jill Kelley was filled with remorse at her complaint’s unexpected impact on Petraeus, a longtime friend. The same forensic techniques that led to Petraeus’ resignation unearthed what Defense Department officials described as 20,000 to 30,000 pages of messages between Kelley and Marine General John Allen, who was deputy chief of the ­Tampa-based U.S. Central Command and then succeeded Petraeus as commander of U.S. and allied forces in Afghanistan. Those astonishing numbers, government experts said, greatly exaggerated the ­frequency of communication because the strict formatting requirements for documentary evidence mandated the inclusion of full headers, signatures and repetitive e-mail chains. Even so, there were at least hundreds of exchanges.

Allen, through associates, denied an affair with Kelley, a married mother of three. Some officials hinted, without specifying how, that the e-mails and other exchanges raise questions of impropriety. The brou­haha was enough to put Allen’s nomination as NATO’s Supreme Allied Commander on hold. While Obama issued a statement expressing confidence in Allen, it is no longer certain who will hold the top U.S. military assignment in Europe.

MORE: Paula Broadwell, David Petraeus’ Biographer and Alleged Mistress

Meanwhile, Kelley’s life and family were singed by the spotlight. Reports cast doubt on the charitable work of the Doctor Kelley Cancer Foundation that Jill and her husband Scott Kelley had established, which spent little of its money on its declared missions “to conduct cancer research and to grant wishes to terminally ill adult cancer patients.” Instead the foundation devoted most of its dollars to meals, entertainment, travel and auto and office expenses. Altogether, Kelley looked as if she were auditioning for the lead in The Real Housewives of Tampa.

The media excavation of the Kelley family fortunes further revealed that Petraeus and Allen took the step, unusual for current and former four-star officers, of intervening in a civilian child-custody case. District of Columbia Superior Court Judge Neal Kravitz found Kelley’s sister Natalie Khawam had misrepresented “virtually everything.” But Petraeus and Allen averred that she was an honorable, loving and reliable mother. Kravitz apparently did not give them much credence. He awarded custody of Khawam’s son to her estranged husband Grayson Wolfe, who once worked for the Coalition Provisional Authority in Baghdad.

By that point the public was obsessed with the details of a case whose players themselves seemed obsessed: law-­enforcement officials revealed that the FBI special agent—Frederick Humphries II, according to the New York Times—who took Kelley’s case to the Tampa field office in the first place had a personal ­friendship with her that included his sending a ­shirtless photograph of himself. Law-enforcement sources said he repeatedly intervened to advance the case, to which he was not assigned, and in late October he telephoned two House Republicans, Dave Reichert and Eric Cantor, to report his ­belief—­erroneous, law-­enforcement officials insist—that Obama’s Justice Department was covering up the case for unspecified political reasons. Humphries, according to the Wall Street Journal, is now the subject of an ethics probe by the FBI’s Office of Professional Responsibility.

(MORE: Beneath Glowing Public Image, Petraeus Had His Critics)

As for Broadwell, she instantly became an object of mass fixation, on everything from her Dickensian name to her fitness  (she out-push-upped Jon Stewart on The Daily Show) to her vast “ambition,” which depending on the headline writer was either an asset or a slur. Everything about the story twisted into knots the standard narratives  about sex and power and values and victims and who exactly gets cast as the protagonist when two married people stray. A homecoming queen from North Dakota whom classmates voted “most likely to be remembered,” Broadwell, like Petraeus, graduated from West Point, with academic, fitness and leadership honors. She earned advanced degrees at Harvard, where she first met Petraeus, and the University of Denver, and she was recalled to active duty three times after 9/11. On Twitter, she describes herself as an author, national-security analyst, Army vet, women’s rights activist, runner, skier, surfer, wife and “Mom!” About three years ago, Broadwell settled in Charlotte, N.C., with her husband Scott, a radiologist in a local medical group, and their two sons. “Yes, I wear a number of hats,” Broadwell told Inspired Woman magazine in February. “But my most important title is mom and wife.”

Discretion or Protection?
Thus far it is undisputed that word of the Petraeus affair first reached the White House on Wednesday, Nov. 7, the day after Obama’s re-election, in a telephone call from Director of National Intelligence James Clapper Jr. to National Security Adviser Tom Donilon. Obama was celebrating with his family and staff in Chicago, and Donilon decided to hold the news until Thursday morning. Hours later, in the Oval Office, Obama told ­Petraeus he was not ready to accept the CIA chief’s resignation. “He wanted to sleep on it,” an Administration official says.

By Friday, there was no saving Petraeus. The Justice Department informed the White House Counsel’s office of the discovery of Allen’s voluminous correspondence with Kelley. Allen’s nomination for the NATO job, with Senate hearings set to begin within days, was put on hold and risked being withdrawn. It was the second time in three days that Obama had been caught unaware by long-simmering investigations within his government. “The President,” said White House spokesman Jay Carney, “was obviously surprised.”

Should Attorney General Holder have informed the President sooner? “I am withholding judgment,” the President told reporters. The unexpected discovery of Petraeus in the Kelley case put the Justice Department in a bind. Nobody wants to return to the days when J. Edgar Hoover used the secrets in his files for political advantage, so deciding what to tell the White House about the private lives of public figures requires great discretion. White House advisers say they are content for the Justice Department to follow its established protocols. But federal officials have offered conflicting and sometimes inaccurate explanations of what the protocols say.

One senior law-enforcement official says a 2007 memo by Bush Attorney General Michael Mukasey set strict limits on White House–Justice communication in criminal investigations. “Alerting the White House of an ongoing investigation? That’s a huge no-no,” the official says.

But the Mukasey memo said something quite different. In criminal cases, it said, Justice should balance the value of secrecy from the “law enforcement perspective” against the information “important for the performance of the President’s duties.” And in national-security cases, the memo specifically stated that no such restriction applied. Mukasey tells TIME that an ongoing extramarital affair by the CIA chief is a potential national-security issue. “They know enough at the point that his name turns up,” Mukasey says. “He’s doing it on a Gmail account, which any intelligence agency in the world would want to know about, and if they did know about, would feel in a position to use.”

MORE: Could Petraeus Face a Court-Martial?

Into the Woods
The voice on the phone was heavy and slow, with a sadness that retired General Jack Keane had not heard from Petraeus before.

“I really screwed up,” Petraeus told his old mentor over the weekend as the scandal swelled around him. That was something of an understatement, as his 37-year career, the future leadership of the CIA, the performance of the FBI and the Attorney General and the career of a top U.S. combatant commander were all suddenly thrown into jeopardy. “This is my fault, and I’m devastated by the pain and suffering that I’ve caused,” Petraeus told Peter Mansoor, one of his old brain-trust colonels. He said that “what he did was a morally reprehensible action,” Mansoor says.

Mistakes have not been a Petraeus hallmark. After graduating from West Point in 1974, Petraeus clambered up the Army’s greasy pole, moving from field assignments to graduate school—he earned a Ph.D. from Princeton in 1987—and serving as an aide to powerful generals, including an Army chief of staff, a NATO military chief and a Chairman of the Joint Chiefs. He began to lap his comrades in 2003, when he led the 101st Airborne into Iraq and north to Mosul. His star rose even higher in 2007–’08, when he returned to Iraq and shifted, midwar, to a counterinsurgency strategy based on protecting civilians with help from a 30,000-strong U.S. troop surge. His success in aborting an Iraqi civil war prompted President Bush to put him in charge of the entire U.S. Central Command in 2008, where he oversaw the wars in Iraq and Afghanistan.

But in military circles, Petraeus had always been a more controversial figure than his reputation suggested. He developed a cultlike staff, which isn’t unusual among generals, though Petraeus’ retinue seemed excessively devoted to their boss. He was as adept at cultivating politicians and reporters as he was at engaging the enemy. Neoconservatives saw him as their standard bearer as the Iraq conflict they had championed bogged down. “Petraeus is a remarkable piece of fiction created and promoted by neocons in government, the media and academia,” argues Douglas Macgregor, an outspoken retired Army colonel. “How does an officer with no personal experience of direct-fire combat in Panama or Desert Storm become a division commander?”

(MORE: The Rise and Fall of ‘General Peaches’)

Petraeus’ move from rock-star four-star to head of the CIA in 2011 came as a surprise in Washington. He had served only a year in Afghanistan and seemed destined to rise to the top of the military at the Joint Chiefs of Staff. But former CIA director Bob Gates told him otherwise: Obama’s White House did not want him in that role. It was Petraeus’ idea, in response, to move to Langley, a close friend says. That solved a lot of problems for Obama, allowing him good use of the general’s talents and diverting him from a possible presidential bid. Cashing in the uniform he had worn since West Point to decamp to the wooded enclave of Ph.D. analysts and hardened spy runners at Langley was not just a dramatic career shift for Petraeus; it was also a move that had little precedent in recent agency history. Gates told Petraeus before he arrived to leave his boarding party behind: past directors who had arrived with an entourage, like Porter Goss and John Deutch, had not been well received. At his confirmation hearings, Petraeus said he’d use his star status to recruit the best agents and analysts available for the agency. He also suggested he would lose his posse: “If confirmed, I will, in short, get out of my vehicle alone on the day that I report to Langley.”

But many senior officers, even those who aren’t as accustomed to aides and horse holders as Petraeus was, can find leaving the Army a challenge, and Petraeus seems to have had some trouble adjusting to the CIA. The agency is strange, rigorous and demanding, as moody as it is secretive. “The agency is not a militaristic organization,” says a senior former intelligence official. “They don’t welcome people barking orders without debate.” Petraeus turned up at one event in a suit with his Army medals pinned to his jacket.

“The Election Played No Role”
By the time Petraeus got to the CIA, Broadwell had been working closely with him for years. Her sugary ­biography of him, titled All In, came out in January 2012. She allowed herself more freedom than most to use nicknames for Petraeus that others might not have chosen to write down: Dangerous Dave, even Peaches. But she was careful to position herself as a serious biographer, not a fan. In a February appearance with celebrity interviewer Arthur Kade, she volunteered, unprompted, “You know, it’s not a hagiography. I’m not in love with David Petraeus, but I think he does present a terrific role model for young people, for executives, for men and women.” Former Petraeus aide and Army Brigadier General Peter DeLuca thinks he understands what happened. “The guy is supergifted, superdetermined, supercommitted. He’s the closest thing most of us have ever met to a superman, but he’s still a man.”

Nor was Broadwell without a larger plan. After running with Lance Armstrong in July, she volunteered her secret purpose to at least six new acquaintances at the Aspen conference. That evening, over drinks, she told a small group that she had been arguing with her mentor about the direction of her career. Republican moneymen, she said, had approached her about a Senate run in North Carolina. She was tempted. Petraeus, she said in an irritated tone, rejected the idea out of hand. What was her position, he asked, on abortion? Climate change? Gun control? Gay marriage? Tax cuts? Social Security vouchers? Her answers, he told her, would not fit either party, and she should not sell herself out.

MORE: Exit Petraeus — and His Famous Military Doctrine

How did Petraeus stay on as top spy after case agents notified FBI Director Robert Mueller last summer that Petraeus was concealing an extramarital affair? And that his e-mail habits were hardly prudent? Vulnerability to blackmail or extortion is usually seen as the paradigmatic counterintelligence threat. After Mueller and Holder were notified, it was about two months ­before the two men dispatched FBI Deputy Director Sean M. Joyce to notify Clapper late on Election Day.

Adultery is prohibited under the Uniform Code of Military Justice. And “depending on timing, it’s very significant for the head of the CIA,” argues Glenn Fine, the Justice Department’s former inspector general. The regulations left Mueller and Holder wide discretion. “We struggled with this,” said a participant in the internal debate, but they satisfied ­themselves early on that “there were no national-­security concerns. He hadn’t been hacked, hadn’t shared classified information, and [other than that] you don’t reveal ongoing criminal investigations, because people get tipped off or there may be investigative things you want to do that are then precluded.” Why, then, tell Clapper about the adultery at all, even when the case was ready to close? “We wrestled with that,” the official says. “Ultimately we made the determination that although we felt there was not a national-security threat, it was for Clapper to know this stuff or somebody to know this stuff and then decide what to do with it.”

(MORE: Petraeus Stumbles Off the Stage)

Agents confronted Broadwell with their findings on Friday, Nov. 2. The agent’s interview report, on form FD-302, did not reach headquarters until late afternoon on Monday, Nov. 5. Mueller and Holder reviewed it the morning of Election Day and decided that the time was ripe for informing Clapper of the case.

Pure coincidence? “The election played absolutely no role,” the official says.

Decline and Fall
There was plenty about the Petraeus affair that played more as farce than as tragedy. But virtually everyone involved exits the stage badly damaged. Jill Kelley’s days as a liaison to any government agency or official are over, a caution to every base commander in the military. Allen’s future is on ice; he may someday become the top U.S. general in Europe, but his nomination is frozen and his fate is now in the hands of a Pentagon investigation that is unlikely to give him an easy pass. The hard-­charging Broadwell denies having unauthorized access to secrets but could face new questions after an FBI search of her Charlotte house. And that discovery, in turn, could raise fresh questions. Did agents miss anything comparable in their parallel investigation into the Petraeus-Broadwell relationship or into the CIA chief’s exposure to hacking risks? The bureau, which for decades has done an excellent job protecting its interests on Capitol Hill, owes the nation accountability for its performance in this most delicate and unpleasant of ­investigations. Some of that should be in open hearings. But only a detailed chronology of the investigation, offered behind closed doors to the relevant committees, should satisfy Congress.

Most troubling is the judgment made at the highest levels of law enforcement not to inform the President. It’s hard to see why Obama wouldn’t expect his FBI director and the Attorney General to inform him when the country’s spy chief is recklessly exposing himself and his mistress to potential blackmail, whatever the special rules and protocols in the binders at Main Justice. That’s common sense in a democracy. The White House says such a call could have raised concerns about political interference, but given the national-security stakes, the absence of a call raises greater concerns about proper Executive oversight of national security.

With regard to Petraeus, who did such an amateurish job of hiding an affair while working as the nation’s top spy, the scandal stunned many in and out of uniform. But it was a measure of how out of touch Petraeus had become that he and apparently a number of other people thought he could stay at the agency after the affair had become known and partially exposed. That is misjudgment of the highest order and has generated considerable shock among former agents and officials, even among those who view Petraeus’ downfall as a personal tragedy. “A lot of power comes from moral authority,” says former CIA boss Michael Hayden, “because you are asking people to do stuff that is really on the edge legally and politically, and they have to sense that you’re the guy they can trust.”

David Petraeus has never been shy or retiring, particularly in a crisis, and it is unlikely that a man who takes his public image so seriously will remain silent for­ever. Friends say he is pondering how best to take responsibility in a fuller, more public way. Until then, the most celebrated general of his generation has just answered the question he famously asked in a very different context nearly a decade ago: “Tell me how this ends.”

with reporting by Massimo Calabresi, Jay Newton-Small, Alex Rogers, Michael Scherer and Mark Thompson / Washington

MORE: For Petraeus, the CIA Was an Uncomfortable Fit

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