Thanks, Robin Raphel :

We Love You in Pakistan

 

 

 

 

 

 

 

   

 

 

 

 

 

 

 

 

 

 

 

 

As Robin Raphel worked for the State Department in Pakistan, her brand of traditional diplomacy ran into the new realities of covert surveillance. The collision turned her life upside down

THE LAST DIPLOMAT

BY ADAM ENTOUS AND DEVLIN BARRETT

Wall Street Journal

 

BEGINNINGS /THE COMEBACK /THE INVESTIGATION THE AFTERMATH

Just before 8 on the morning of Oct. 21, 2014, Robin Raphel climbed into her Ford Focus, put her purple briefcase on the passenger’s seat and began the 20-minute drive from her house in Washington to her office at the State Department.

It was a routine Tuesday. The main event on her schedule was a staff meeting.

Raphel swiped her badge at the revolving security door and headed to her office where she placed her briefcase on the floor and sat down to check her email. Later, as she joined her colleagues in a conference room to discuss office schedules, her mobile phone, which she had left at her desk, began to ring. It was Slomin’s Home Security.

When she didn’t pick up, the operator called her daughter Alexandra, who raced to the house to check the doors and windows. When Raphel returned to her desk, the phone rang again. It was Alexandra, in a panic.

Burglars hadn’t set off the alarm. It was the Federal Bureau of Investigation.

Raphel grabbed her purse and ran out. She left behind her purple briefcase—one she had bought at the Kohsar Market in Islamabad—with a bag of carrots and a Rubbermaid container full of celery sticks inside.

As she pulled up to her yellow-brick house, Raphel saw agents going in and out the front door, walking across the oriental rugs she had trundled back from tours in South Asia. They boxed up her two computers, Alexandra’s iPad and everything else electronic. In the basement, they opened the drawers of a mahogany file cabinet she had picked up during a posting in London. They pulled out a stack of files.

The agents, without saying a word, carried the boxes out to a white van.

Raphel, unsure of what was happening, paced in circles on her front porch.

Two FBI agents approached her, their faces stony. “Do you know any foreigners?” they asked.

Raphel’s jaw dropped. She had served as a diplomat in six capitals on four continents. She had been an ambassador and the State Department’s assistant secretary for South Asian affairs. Knowing foreigners had been her job.

“Of course,” she responded, “Tons…Hundreds.”

Three weeks before the FBI raided her house, Raphel had touched down at Benazir Bhutto International Airport in Islamabad. The city was in an anxious, turbulent state. Antigovernment protesters had closed off so many streets that her driver had to take a roundabout route to the diplomatic quarter.

All summer, U.S. intelligence agencies had been intercepting rumors from Pakistani officials about a possible coup. Alarm bells were ringing in the State Department’s office of the Special Representative for Afghanistan and Pakistan, where Raphel worked and went all the way to the White House. She had come to figure out what was really going on.

In her apartment at the embassy, she found a bottle of wine—a welcoming gift from U.S. Ambassador Richard Olson, who was thankful for her help in an uncertain time.

At a dinner party at the home of an American diplomat in Islamabad’s elite E-7 sector, Raphel and a group of Pakistani politicians pulled their seats into a circle in the living room to discuss the rumors. One parliamentarian said he was bullish on the idea of the populist opposition leader Imran Khan taking power. A former Pakistan ambassador to Washington countered that Khan had moved too soon and predicted the sitting prime minister would survive.

With students at Damavand College in Tehran, 1971With Arnold Raphel at a cocktail party in Islamabad, Before leaving, Raphel reported her findings to the ambassador. Pakistan was prone to coup talk, she knew, but she didn’t believe the current conditions were right for an overthrow of the government. In the end, she was correct: The rumors had been overblown. Khan’s followers would soon disperse, and Nawaz Sharif would remain prime minister. She had flown home considering her trip productive.

Over a four-decade career in the foreign service, whether in Islamabad, London, Pretoria, New Delhi or Tunis, Raphel had distinguished herself by building vast networks of contacts. She had spent as much time as she could outside the embassy, rubbing shoulders with politicians, military officers, journalists, aid workers and spies over teas, lunches, and endless cocktail parties. Sources felt they could talk to her—that she understood them.

Nowhere was that more true than in Islamabad, where she had started her diplomatic career. “I could go to Robin and say, ‘does this member of parliament matter?’ ” said Cameron Munter, who took over as U.S. ambassador to Pakistan in 2010. “She knew them all.”

There was a downside to being trusted in a country that many of her colleagues in Washington loathed. Those who took a dimmer view of Pakistan, especially in intelligence circles, were suspicious of Raphel’s close connections in Islamabad. They believed she had become too close to the Pakistanis and that she was being used.

In moments when the two countries were at odds, Raphel had consistently argued against pulling up the drawbridge. In conference calls with Washington, her co-workers said, she would always say: “Let’s look at it from their point of view.” As early as the mid-1990s, intelligence officers saw her as an obstacle to isolating Pakistan over its nuclear program.

“For better or worse, she got a reputation within the intelligence community as tilting towards the Pakistanis, and she could never escape that,” said Bruce Riedel, a CIA veteran who served as deputy assistant secretary of Defense for the Near East and South Asia in the 1990s.

Unbeknownst to Raphel, as she had made her rounds in Islamabad in the fall of 2014, and spoke to contacts on the phone and on Skype, law-enforcement officials half a world away had been listening. Raphel’s old-fashioned way of doing business—working outside the confines of the embassy compound—had run headlong into the realities of America’s global surveillance web, on which the U.S. had increasingly come to depend on.

Since receiving a tip from an intercepted communication months earlier, the FBI had obtained warrants to monitor Raphel’s private accounts and to secretly search her home. They had transcribed information she had discussed with Pakistanis and taken it to intelligence officials, who had told them the topics were beyond her security clearance. The message, according to a former senior intelligence official, was that “Robin needs to shut up.”

What they heard during her trip to Islamabad had been the final straw. Law enforcement officials said the people listening were convinced Raphel was a threat to national security.

The following account of the FBI investigation of Raphel is based on interviews with dozens of her co-workers, Pakistani contacts, intelligence officials, law enforcement officers and attorneys involved in the case.

PART 1BEGINNINGS

When she landed in Tehran in 1970 to teach at a women’s college, Robin Lynn Johnson was 23, a native of the small lumber town of Longview, Wash., whose curiosity about the world had grown from reading her father’s collection of National Geographic magazines and historical novels. With blond hair, high cheekbones and a posture honed through years of ballet, she sometimes drew comparisons to the actress Candice Bergen.

There, she met Arnold Raphel, a political officer at the U.S. embassy. Arnold stood 6-foot-1, a full head taller than Robin. He wore aviator-style wire-rim glasses with conservative suits, giving him a perpetually serious look, though he was anything but. Wherever he went, a party seemed to erupt.

Tehran was in the throes of an oil boom and the young couple spent their nights dancing on the wraparound porch at the Naderi hotel, where the city’s elite turned out in the latest Paris fashions. In 1972, when Robin was 25, she married Arnold on the grounds of the U.S. embassy, which, just eight years later, would be overrun by followers of the Ayatollah Khomeini.

 

Raphel’s wedding to Arnold Raphel in Tehran in 1972. 

Posted to Islamabad in 1975, the Raphels were prolific entertainers, former colleagues remembered. Over cocktails and private screenings of American movies flown in by the U.S. military, they began to unravel Pakistan’s social and political dynamics. It was then that Raphel started to get a sense of what a confusing place Pakistan could be.

Islamabad wasn’t an easy place for diplomats to operate, much less comprehend. Double talk reigned—to the point where even veterans of the game couldn’t tell who was pulling the strings, or who was manipulating whom. Because most high-ranking officials there spoke English, many diplomats from both sides “made the mistake of thinking we’re speaking the same language, when we are not,” said Marc Grossman, who served in Islamabad with the Raphels in the 1970s. “Sometimes we live on entirely different planets.”

When the Raphels returned to Washington in 1978, Robin wanted to have children. Arnold, who had a daughter whom he rarely saw from his first marriage, did not. They divorced in 1982.

Six years later, Arnold, who returned to Pakistan as the U.S. ambassador, was killed in a mysterious plane crash with then-Pakistani President Muhammad Zia al-Haq.

Though she married twice after Arnold and had two daughters, Raphel never changed her name. She told colleagues that this was how everyone knew her professionally. Because of Arnold’s stature, the Raphel name carried huge prestige in Pakistan. One of Raphel’s oldest friends said he thought she kept the name because “Arnie was the love of her life.”

In 1993, President Bill Clinton, an acquaintance from her university days, tapped Raphel to serve as the nation’s first assistant secretary of State for South Asian affairs. Eighteen years after she first arrived in Islamabad as the young wife of a diplomat, Raphel found herself at the center of the action.

During her first trip to Islamabad as assistant secretary, Raphel visited the Foreign Ministry, a whitewashed building surrounded by manicured lawns. There she met a woman named Maleeha Lodhi, who had just been named Pakistan’s ambassador to the U.S.

MALEEHA LODHI

Lodhi met Raphel in 1993 after she was tapped to serve as Pakistan’s ambassador to the U.S. for the first time. Raphel and Lodhi turned to each other, on and off, for information. In 2014, the FBI became suspicious of their relationship. Editor of The News, a prominent English-language paper in Pakistan, where her front-page foreign policy columns had made her a star.

At her home in Islamabad, Lodhi fostered a salon-like atmosphere where politicians, intellectuals, and journalists listened to music and debated the news long into the night. Pakistan’s new prime minister, Benazir Bhutto, would sometimes make an appearance. Raphel’s colleagues from the U.S. embassy, who attended some of these sessions, had concluded, based on the assembled guests, that Lodhi was a serious player.

Lodhi wasn’t from one of the prominent families that typically produced the country’s top leaders. She learned English from Irish nuns at a convent in Rawalpindi, where she grew up in an upper-middle-class home, the daughter of an oil company executive. She made her way to England, where she studied at the London School of Economics. Tim Carney, who served as Raphel’s deputy, said he always knew where he could find Lodhi at parties—outside in the middle of a boisterous crowd, smoking Cartier cigarettes.

Lodhi was drawn to Raphel. She knew that Raphel’s State Department title and her position as a friend of President Clinton would be useful to her in navigating Washington.

Raphel found Lodhi to be intelligent, ambitious and serious—if a bit reserved. She also recognized her as someone who would be a longtime influencer.

“Pakistan is a country of 200 million people. But its leadership is like a deck of cards,” said Husain Haqqani, the former Pakistani ambassador to Washington. “However you shuffle them, the same 52 people will show up in one hand or another. Robin understood that.”

Lodhi’s ambassadorial residence in Washington was a short walk from a Ritz-Carlton Hotel, where she liked to meet Raphel and other friends next to the lobby fireplace. Lodhi was 10 years younger than Raphel but the two women had a lot in common. Like Raphel, Lodhi was a single mother—she had married a Pakistani civil servant at 25 and divorced five years later. Both had strong opinions and didn’t hesitate to share them, and were climbing the rungs of power in a profession dominated by men.

In 1995, Congress took up the Brown Amendment, a piece of legislation that would begin to ease nuclear sanctions it had imposed on Pakistan. The two women joined forces in a monthslong lobbying campaign to support it.

For Lodhi, the bill’s passage helped build her credibility as a diplomat. Raphel considered the victory to be one of the signature accomplishments of her time as assistant secretary—but it also came at a price. The Brown Amendment, which President Clinton supported, had not been popular with some U.S. intelligence officials, who believed the U.S. should isolate Pakistan to pressure its leaders to end its nuclear program. Raphel took the brunt of the backlash.

Not long after the amendment passed, Deputy Secretary of State Strobe Talbott sent an aide to Raphel’s office with a disturbing message.

According to officials, the aide told Raphel U.S. spy agencies had intercepted communications in which Pakistani officials suggested that Raphel had revealed sensitive information to them about what the U.S. knew about Pakistan’s nuclear work. U.S. intelligence officials said the information was classified and the disclosure wasn’t authorized.

Raphel denied disclosing too much. She consulted with top officials at the State Department’s internal intelligence branch, who recommended she ask Diplomatic Security—the security and law enforcement arm of the State Department—to investigate the matter.

Diplomatic Security agents interviewed Raphel about the alleged disclosures. They found no evidence of wrongdoing and took no disciplinary action against her. But Raphel was rattled.

To provide “insurance” in case the allegations re-emerged, she later told friends, she took the relevant records, including papers marked as classified, and put them in her safe at the State Department.

Raphel, dressed for the Marine Ball in Islamabad, in 1975. 

In 2003, Raphel took a posting in Baghdad, where she helped steer Iraq’s postwar reconstruction in the teeth of a violent insurgency. She would don a head scarf and jump into local taxis to see Iraqi officials or drive to meetings alone in her SUV.

“Robin was the type that did what she knew had to be done and asked for forgiveness later,” said retired Lt. Gen. Jay Garner, one of her bosses in Iraq. “She lived on the edge but she never fell off.”

After two years of working on Iraq, Raphel had seen the insurgency hollow out much of the work the U.S. had done. She decided it was time to leave the State Department.

On the day before her 2005 retirement ceremony—which was held in the State Department’s Treaty Room—Raphel packed her books, mementos and photographs into boxes, along with the contents of her office safe, and took them home.

The next day, after the toasts and speeches had ended, Raphel had a plane to catch. She was due to appear at a conference in Dubai. She went to the basement and opened her mahogany file cabinet. She dumped the papers inside.

Raphel came from a generation of diplomats whose approach to the job had been honed in a different time. America’s presence in the world was changing.

Since 9/11, security concerns abroad had forced diplomats in volatile parts of the world to spend more time cooped up in fortified embassies. The volume of “human intelligence” or “humint” they gathered by talking to contacts began to decline. In its place, policymakers in Washington turned to another form of information—the kind collected electronically and surreptitiously.

To monitor foreign governments around the world, the U.S. uses satellites and ground-based sensors implanted in local communications networks that sweep electronic communications and reroute them to the U.S. Most of this information, known as “signals intelligence,” or “SIGINT,” is funneled into a steel and glass building 25 miles north of the State Department in Fort Meade, Md., the headquarters of the National Security Agency.

The Urdu-speaking analysts who covered Pakistan at the NSA sat in cubicles and worked in shifts listening to audio files that stacked up in queues on their computer screens like emails. To help them follow the conversations on their headphones, sound waves bounced on their screens. The analysts tracked political, military and economic developments in Pakistan, just like the diplomats, but by targeting the email addresses and phone numbers of senior officials, many of whom were also Raphel’s contacts. If they heard something of intelligence value, analysts wrote summaries that were compiled into signals-intelligence reports and disseminated to senior policy makers.

Raphel greeted Pakistani Prime Minister Benazir Bhutto. Maleeha Lodhi stands on the stairs of the plane. 

Making sense of these conversations wasn’t easy, especially in Pakistan. U.S. analysts who covered the region often felt as if they had entered a hall of mirrors. The cryptic and deceptive nature of talk between Pakistani officials—who often knew they were being monitored—made it difficult to understand the context or judge the veracity of what they were saying.

Often, U.S. diplomats would read signals-intelligence reports and realize the Pakistanis were misreporting what Americans had told them, either because the messages were unclear, mistranslated or simply misunderstood—or because they were twisting them on purpose for professional or political reasons.

Among Pakistani diplomats, “The desire to tell your bosses what they want to hear is overwhelming,” said Haqqani, the former Pakistani ambassador.

As the NSA’s techniques grew more sophisticated, and as the business of government increasingly shifted to email and mobile phones, the volume, and quality of the intercepts grew. The information in these reports was so immediate and uninhibited—and often so salacious—senior officials could hardly wait to read them. In the four decades since Raphel joined the State Department, and especially during the Obama administration, officials say, the U.S. government’s reliance on signals intelligence had grown to the point where it made up anywhere from 60% to 75% of the information coming in. And yet it was impossible to know how much of it was reliable.

“You always have to be careful because you’re listening to a conversation. You aren’t listening to testimony. You aren’t listening to a brief that’s fully thought out,” said former NSA Director Michael Hayden. “You are trying to determine truth from a conversation that is oblique, indirect and casual, often in a language not your own and in a culture that you do not share.”

In 2009, as the Obama administration stepped up its drone war in Pakistan’s tribal areas, a staging ground for militants to launch cross-border attacks on U.S. forces in Afghanistan and to plot against the West, the embassy’s clandestine function became the top priority.

Four years into her retirement, Raphel was working as a lobbyist in Washington. Settled at home, with three ill-fated marriages behind her, she had more free time to spend with her two college-age daughters, Alexandra and Anna, and to take long walks with friends along the towpath in Georgetown.

She enjoyed her downtime but had grown tired of scaring up clients and tracking billable hours as a lobbyist.

In the spring of 2009, when she was 61, Raphel attended a cocktail party in Washington where she bumped into an old friend: Anne Patterson, the sitting U.S. ambassador to Pakistan. When the subject turned to Patterson’s work at the embassy, Patterson told Raphel she didn’t have enough people who really understood Pakistan’s complexities. Patterson often told aides that Islamabad was the “weirdest” place she had ever served.

ANNE PATTERSON

Ambassador Patterson ran into Raphel at a dinner party in Washington in 2009 and asked her to join her team at the U.S. embassy in Islamabad. Patterson held up Raphel as a model to more junior foreign-service officers because of her long list of Pakistani contacts.

Pakistan had also become a more dangerous place for diplomats. One year earlier, terrorists had detonated a dump truck full of explosives at the Marriott Hotel, killing more than 50 people and carving a 60-foot crater in the ground. Much of Patterson’s time as ambassador had been devoted to overseeing the CIA’s covert drone strikes on militant targets.

The State Department’s Diplomatic Security service, charged with protecting the U.S. embassy in Islamabad, had grown so concerned about terrorism that the compound was often put on lockdown. Fewer embassy workers ventured out and usually only then in U.S. armored vehicles. For security reasons, the State Department had begun to limit foreign-service officers in Islamabad to one-year tours, giving them barely enough time to acclimate before shipping out. Many officials spent their time in a secure room reading signals-intelligence reports or working on their suntans by the pool.

Patterson knew Raphel wasn’t one for the “Fortress America” style of diplomacy that had taken root after 9/11, in which monitoring for threats was the top priority. Patterson needed someone to help manage billions of dollars in U.S. aid money aimed at shoring up the country’s new civilian-led government—someone who could open doors and who had deep connections within the country’s power structure. She asked Raphel if she would consider coming back.

Raphel liked the idea of serving her country again and asked Patterson for time to think.

She called one of her oldest friends from the State Department, Beth Jones, to ask her advice. “Go for it,” said Jones, who added that it sounded like an opportunity to do “things that really mattered.” A few days later, Raphel accepted the job.

PART 2   –   THE COMEBACK

In August 2009, Raphel moved into a white, two-story stucco house on First Street in Islamabad’s F-6 neighborhood.

Like every house on First Street, it was built in the 1960s, when Pakistan laid out its capital. It had a high-security wall topped with shards of glass. Unlike most other houses, however, it also had bars on the windows.

What the house lacked in curb appeal, it made up for in proximity. The outdoor cafés of the Kohsar Market, where Pakistan’s political class gathered in the evenings to trade conspiracy theories over fruit drinks and sandwiches, were a five-minute walk.

After settling in, Raphel went to a website that specialized in inexpensive, refurbished right-hand drive Japanese cars and purchased a silver Toyota—a kind that is ubiquitous in Pakistan. She figured it wouldn’t stand out and that she could use it to roam the city freely.

Dressed in a long traditional Pakistani tunic known as a kameez, worn over a pair of loose, lightweight trousers, or shalwar, she would drive herself to party after party in Islamabad, something few of her embassy colleagues would ever do. One of her bosses referred to her as “the last of the Mohicans.”

In the 1990s, when she was the State Department’s assistant secretary for South Asian affairs, Raphel had been the one shaping U.S. policy on Pakistan. Now, her superiors in Washington, many of whom were much younger and didn’t know the country as well as she did, were calling the shots.

 

In Islamabad, however, the power players had barely changed and she fell quickly back into the whirl. In the evenings, she would huddle with local journalists at café tables in the Kohsar Market. One day she would meet with Gen. Ashfaq Parvez Kayani, the powerful army chief, to talk about aid projects, then fly to Lahore or Karachi to sit down with television talk-show hosts, bureaucrats and businessmen the next, all with a level of informality and directness that came from spending so many years in the country.

By the end of her last tour there, Raphel had become such a ubiquitous figure, and so widely trusted, that many Pakistani officials mistakenly believed she outranked the ambassador. “You weren’t talking to a U.S. diplomat,” explained Abid Hasan, a former World Bank official in Islamabad. “You were talking to Robin.”

In Islamabad, Raphel’s job was to focus on aid projects. But she also “delivered the mail,” as State Department officials say, for other diplomats who didn’t have her level of access. In that informal role, co-workers recalled, Raphel was sometimes asked to raise issues that went beyond her remit.

The NSA regularly swept up Pakistani communications “to, from or about” senior U.S. officials working in the country. Some American officials would appear in Pakistani intercepts as often as once a week. What Raphel didn’t realize was that her desire to engage with foreign officials, the very skill set her supervisors encouraged, had put a target on her back.

As Raphel settled into Islamabad, she was reunited with Maleeha Lodhi, and the two women fell back into their working friendship. Once again, Lodhi became one of Raphel’s best contacts, and Raphel, in turn, became one of Lodhi’s.

Lodhi was out of government. She had returned to the news business, writing a regular column and appearing as a commentator on Pakistani television. American officials said they had no doubt that Lodhi was more than an ordinary journalist, however.

In her six years in Washington as Pakistan’s ambassador, Lodhi had earned a reputation as a reliable source for what Pakistani officials were thinking, and in particular, as a trusted conduit for relaying messages to Pakistan’s senior military leadership in Rawalpindi, U.S. officials said. She was, in State Department parlance, an “influencer.” One reason U.S. officials trusted her: The NSA had long been monitoring her communications.

Pakistani officials with ties to Lodhi said the Americans exaggerated her influence. They said she was a journalist first, not a go-between. If she picked up something interesting in a conversation, she would occasionally share it with her Pakistani military contacts, but only if they reached out to her.

“Yes, she was in this game of information,” one of the officials said. “American diplomats would ask her, ‘What’s the thinking here?’ Others would ask, ‘What do you think the Americans will do next?’ ”

When Raphel and Lodhi met, Lodhi would take notes. Officials close to her said they were for her newspaper columns. The Americans said the notes were for reports she would send to government and military officials. Raphel, always concerned with maintaining informality, kept her notebook in her purse, and scribbled down information once she got back to her car.

Raphel’s boss was Richard Holbrooke, who had been named to a new role in the State Department—the Special Representative for Afghanistan and Pakistan, or SRAP. Holbrooke encouraged his team of advisers to embrace “creative chaos,” work through informal channels and bypass government bureaucracy to get things accomplished.

RICHARD HOLBROOKE

A diplomatic troubleshooter who sought to forge a political solution to the war in Afghanistan, Holbrooke encouraged his advisers to work outside established diplomatic channels.

U.S. intelligence officials had always chafed at the way the State Department handled sensitive information. They long suspected Pakistani diplomats in Washington tried to pry information out of the SRAP office, viewing it as more forthcoming than other departments—a charge SRAP officials deny. From the perspective of intelligence agencies, including the FBI, the very existence of the Holbrooke team, working outside regular channels, “was a disaster waiting to happen,” said one former law-enforcement official.

After Cameron Munter took over as the U.S. ambassador to Pakistan in 2010, the competing forces of intelligence and diplomacy began to collide. When Munter pushed the CIA to be more “judicious” in its drone strikes in the tribal areas, the CIA’s station chief responded by telling diplomats not to discuss the drone program even in private meetings with senior Pakistani officials. If asked, he told them, they should change the subject.

Senior diplomats in Islamabad knew this was impossible. The drone program came up all the time. There was no way to avoid the topic.

Raphel didn’t know the key details because her Top Secret clearance didn’t include access to the “compartment” that covered the covert program. When her Pakistani contacts complained about the strikes, Raphel told them what other diplomats would say—that the U.S. wouldn’t need to do so many if the Pakistani army did more to rein in militants in the tribal areas, according to people she spoke with.

She would argue drones caused less collateral damage than the alternatives: American ground troops, Pakistani artillery strikes or F-16 bombing runs.

The populist politician Imran Khan, the loudest advocate in Pakistan against the drone program, said he had two sit-downs with Raphel in which he protested the strikes and that Raphel came across as “sympathetic” to his concerns. “I actually didn’t know what her position was, but I thought that I could make her understand me,” he said.

In December 2010, Holbrooke died of a torn aorta. In his absence, hard-liners in Washington who saw Pakistan as the enemy worked to undo many of his team’s efforts, officials said.

The deaths of two Pakistanis at the hands of a CIA contractor inflamed tensions between the countries. Then, in May of 2011, U.S. commandos violated Pakistani airspace during a mission that killed Osama bin Laden, setting off a new furor.

With the CIA’s influence growing larger, and the U.S.-Pakistan relationship crashing down around her, Raphel urged the State Department to keep working hard to maintain strong ties. “Everyone else wanted to take a hard line against the Pakistanis,” Munter remembered. “She was saying, ‘We want to salvage what we can because it is so important.’ ”

As she managed the U.S. aid program, Raphel spent a little time in her embassy office. Sometimes she would leave her calendars and other papers on her desk instead of locking them away for the night. Marines who policed the embassy for security infractions cited her for these lapses. After three citations, Raphel received a reprimand from the State Department. Though it was a boilerplate letter many diplomats receive and represented the lowest level of sanction the department could take, its language sounded ominous to outsiders. It went in her personnel file.

With Afghan Foreign Minister Amin Arsala, Kabul, 1993Raphel after flight in training aircraft in Tunisia, 1998With Pakistani interim Prime Minister Moeen Qureshi, Indian Ambassador Siddhartha Shankar Ray and Indian Finance Minister Manmohan Singh, Washington, 1993Beside a fallen statue from Saddam Hussein’s palace, Baghdad, 2004With Nelson Mandela in Tunis, 1999

 

After the bin Laden raid, Raphel emerged as one of the few U.S. diplomats the Pakistanis were still eager to talk to. As Pakistanis scaled back contacts with American officials, “doors would still open for her,” said Mushahid Hussain Sayed, a prominent Pakistani senator.

As her tour in Islamabad was nearing its end, then-President Asif Ali Zardari invited Raphel to his residence for a private dinner, a signal he was ready to re-engage after the bin Laden raid. Munter, the ambassador, wasn’t invited.

After two years in Pakistan, the deterioration in relations made it harder to get aid projects done. Raphel was offered a new post in Washington as an adviser to Marc Grossman, who had replaced Holbrooke. Her new job was to collect political intelligence on Pakistan and help explain U.S. policy to officials there.

Before Raphel’s frequent trips to Islamabad, Grossman’s team would sit down with her to create a detailed itinerary of whom she would see and what she would tell them, her friend and diplomatic colleague Beth Jones recalled. Despite her past experience, Raphel had been excluded from the White House’s secret talks with the Afghan Taliban, and when high-level meetings took place at the Pakistan embassy, she wasn’t invited.

In Islamabad, the dynamics were different. Many Pakistanis still considered her to be the central player she was in the 1990s. Some of Raphel’s friends complained about the Obama administration’s approach to Pakistan. They thought Raphel was the one who should be formulating U.S. policy. The NSA picked up Lodhi and others criticizing Raphel’s superiors, officials said.

Though she scheduled her official meetings through the embassy and typically brought a note-taker, Raphel had fewer people to check in with and fewer constraints on her movements. She usually reported what she learned to a small number of senior State Department officials in informal emails that weren’t widely disseminated.

Some of the regular U.S. embassy diplomatic staffers, more isolated than ever, resented Raphel’s easy access. They seized on the old complaint that she was too quick to see things from Pakistan’s perspective. Over drinks at the American Bar at the embassy, said a senior official who worked there during Raphel’s final tour, “they badmouthed her. She was disrupting their comfort zone and they didn’t like it and they assumed she was doing something wrong.”

On Nov. 26, 2011, U.S. forces in Afghanistan accidentally attacked two Pakistani military checkpoints along the Afghan border, killing about two dozen Pakistani soldiers. Pakistan responded by blocking the Pentagon from using land routes to resupply U.S. and international forces in Afghanistan. Pakistan demanded an apology. The White House refused.

Raphel was exasperated. She couldn’t believe the U.S. would risk its relationship with Pakistan by failing to acknowledge what had clearly been a mistake. “We have to do this,” she would tell senior officials.

In January, in an email to her boss, Raphel wrote that in Pakistan, “The lack of a U.S. apology for the 24 dead still rankles very deeply.”

During her trips to Islamabad, Raphel was often more candid about her views with Pakistani officials, whom she felt comfortable confiding in, several of her colleagues said.

Raphel knew what intelligence analysts did at the NSA. She knew that when they swept up phone calls and emails from the Pakistanis she met with, they might see accounts of the things she had said. Some of her co-workers say she should have realized that her private comments would be reported by the Pakistanis and potentially twisted. They figured she might get in trouble for this.

They didn’t think anyone would accuse her of espionage.

PART 3   – THE INVESTIGATION

As Raphel settled back into her house in Northwest Washington in 2011, spy fears at home had soared to heights not seen since the Cold War. After an Army intelligence analyst leaked thousands of classified diplomatic cables, the White House issued an executive order establishing a governmentwide program to deter and detect “insider threats.”

President Barack Obama gave U.S. spy agencies and the FBI a one-year deadline to put the crackdown into motion.

By the time Edward Snowden leaked classified documents detailing the NSA’s global operations in 2013, the pressure to catch government moles had increased exponentially, former FBI officials say. The bureau was eager to bring cases.

Hunting for spies and moles had long been one of the FBI’s most secretive, time-consuming, complex and unpopular assignments. Many of the bureau’s counterintelligence agents worked out of a field office in Washington, in specially designed spy-proof rooms without internet access where they read the daily bounty of signals intelligence for anything that suggests an American shared classified information.

When analysts at the NSA heard chatter about classified information, they would send the FBI what is known as an “811 referral.” Of the hundreds of these referrals the bureau receives in a year, its agents typically investigate one in five.

In February 2013, according to law-enforcement officials, the FBI received information that made its agents think Raphel might be a Pakistani mole.

The tip came in the form of intercepted communications that suggested Raphel had shared sensitive inside information without authorization. Two officials said this included information collected on wiretaps of Pakistani officials in the U.S.

Two FBI agents—a man and a woman—were assigned to investigate. Both were experienced in so-called “65 work,’’ FBI-speak for espionage cases. One of the agents had past experience investigating alleged Pakistani spying. The other had done 65 work involving Israel.

Investigators began what they call “circling the target,” which means examining the parts of Raphel’s life they could explore without subpoenas or warrants. Sitting in their cubicles on the fourth floor of the FBI’s Washington Field Office, a modern sandstone-colored building on the edge of Chinatown, the agents began to map her network of contacts and search for signs of disloyalty.

One of the first things they looked at was her “metadata”—the electronic traces of who she called or emailed, and also when and for how long. Her metadata showed she was in frequent contact with a host of Pakistan officials that didn’t seem to match what the FBI believed was her rank and role.

The agents didn’t talk to the State Department officials who oversaw Raphel’s work. Instead, they approached the head of Diplomatic Security, Gregory Starr, to gain access to her personnel files and other records. Starr, in turn, kept State Department leaders who knew Raphel in the dark, worried about compromising the FBI investigation, State Department officials said.

State Department files showed she had been formally reprimanded for security infractions while working at the embassy in Islamabad. Over the course of her career, going back to 1977, she had been cited more than a dozen times. Raphel’s colleagues said this was a minor issue, considering her decades on the job. To the FBI it was a red flag.

After months of circling the target, FBI supervisors decided it was time to delve deeper. To monitor Raphel’s private conversations with Lodhi and other contacts on Skype, the FBI obtained a warrant from the Foreign Intelligence Surveillance Court—a decision approved at the highest levels of the FBI and the Justice Department.

 

The agents dug into her personal life. They probed her finances and looked at who was making college tuition payments for her daughters. The agents wanted to see if the Pakistanis might be covering her bills. They noticed when Raphel was a lobbyist, she had once registered as a “foreign agent” in order to lobby for Pakistan.

The FBI didn’t have a clear picture of where Raphel fit on the State Department organizational chart. She was a political adviser with the rank of ambassador but she wasn’t a key policy maker anymore. She seemed to have informal contacts with everyone who mattered in Islamabad—more, even, than the sitting ambassador and the CIA station chief.

The sheer quantity of Raphel’s communications on the thorniest issues of the day raised suspicions for the FBI agents who were reading the transcripts.

The agents investigating Raphel didn’t have extensive experience dealing with State Department diplomats. They had even less exposure to diplomats of Raphel’s generation. By the way, she spoke, Raphel sometimes made it sound as if she was giving Lodhi and other Pakistani contacts extremely valuable information.

For months, the agents read emails, pored over records and listened to intercepts to try to learn whether Raphel was giving away U.S. secrets. While they didn’t find any smoking-gun evidence of wrongdoing, there was plenty of “smoke,” one former law-enforcement official said. The FBI decided it was time to up the ante.

In January 2014, the bureau obtained a court-issued “sneak and peek” warrant, allowing agents to secretly search Raphel’s northwest Washington home while she was away.

The FBI sent a special Evidence Response Team trained in surreptitious searches. Raphel’s home had an alarm system, which the FBI team bypassed. Once inside, agents searched the living room and the three bedrooms. From the kitchen, they descended the stairs into the basement where they found the mahogany file cabinet.

When the FBI agents looked inside, they discovered the 20-year-old classified documents from Raphel’s Diplomatic Security investigation—a group of papers officials would later refer to as “the nuclear file.”

The agents put everything back as they found it. At the least, they believed they had enough evidence to pursue charges against Raphel for the crime of mishandling classified information. The agents thought they could be dealing with a decades-old asset of the Pakistani government, and suspected Maleeha Lodhi, who had been a figure in her life since the 1990s, was her point of contact.

In the same month, the FBI searched Raphel’s house, James Comey, the new FBI director, visited a field office in Birmingham, Ala., where reporters asked him if the government was spying on people.

JAMES COMEY

Comey became the director of the FBI in September 2013. The Raphel investigation had already begun at that point, but Mr. Comey oversaw and approved key decisions to proceed further with the case. Earlier this year, speaking about the Clinton email investigation, Mr. Comey faulted the “security culture” of the State Department when it came to protecting classified information.

He said no—with a caveat. “Well, not the average person…Now, if you’re involved in one of the things I’m worried about if you’re trafficking drugs, if you’re involved in violent crime, if you’re a terrorist or spy, I would like to be spying on you because I need to know what you’re doing,” he said. “That’s our business.”

While the FBI agents conducted their own surveillance, the bureau approached the NSA for assistance in gathering foreign intercepts involving Raphel and emanating from Islamabad, law-enforcement officials say. They were looking for what they call “flags on the target.”

The FBI’s suspicions were piqued, the officials said, when in some intercepts, Pakistanis referred to Raphel as a “source,” rather than by name. To the investigators, it sounded like spycraft.

The agents listening to the back-and-forth between Raphel and Lodhi and her other contacts were struck by what law-enforcement officials described as the “one-way” nature of the conversations. It seemed to the FBI as though Raphel did most of the talking and provided most of the information. One law-enforcement official said Raphel appeared in those discussions to be what cops sometimes call a “hip pocket source’’—not a formal intelligence asset or informant, but a “friendly’’ who was willing to share the information she came across informally.

As the agents listened to the back-and-forth, they would check with U.S. intelligence officials to see if the topics which Raphel discussed with Lodhi— drones, coups and reconciliation talks with the Taliban—were classified. They were repeatedly told that yes, they were.

FBI officials could have raised concerns about Raphel’s communications with her State Department superiors to get her to back off, but they didn’t. They wanted to catch her in the act, officials said.

For the FBI, the tipping point was Raphel’s trip to Islamabad where she looked into the coup rumors.

During her visit, Raphel was in regular phone contact with Lodhi, who invited her to come to her home library to talk privately over tea. Officials briefed on the investigation said the information they exchanged during the trip about the prospects of a coup was similar to what U.S. spy agencies were picking up—the same kind of information that intelligence officials were putting in the President’s Daily Brief.

The agents at the FBI’s Washington Field Office decided it was time to confront her.

As Raphel stood on the small porch of her house in Washington on Oct. 21, 2014, the FBI agents leading the raid asked her for the names of the Pakistanis she spoke to most.

Raphel mentioned the Pakistani ambassador to the U.S., Jalil Abbas Jilani. She told the agents she had known him for a long time and that he was her primary contact. She didn’t mention Lodhi.

The agents, who had been monitoring her conversations for more than a year, thought she was being evasive, according to law-enforcement officials. They asked Raphel if she had any classified documents in her house. She said she didn’t.

The agents were holding some documents during the conversation. The male agent flashed one of the pages. She could see that it bore classification markings.

Raphel’s mind was spinning. She told the agents that she had taken the classified documents home in 2005 and forgotten about them.

The agents didn’t think she offered a clear reason as to why she would have the authority to possess them.

As the conversation went on, the agents’ questions became more aggressive. Raphel started to think about lawyers she knew.

Beth Jones heard from a mutual acquaintance that something bad was happening to Raphel. Jones called her office phone but got no answer. She tried her mobile, and Raphel picked up right away. “What in the world is going on?” asked Jones.

Raphel told her FBI agents were going through all of her personal things, and that Alexandra was terrified. “I don’t know what this is all about,” Raphel said.

“It must be some horrific mistake,” Jones said.

The agents saw Raphel talking on her cell phone on the porch. They asked her to hand it over.

Back at the State Department, as Raphel’s co-workers watched, plainclothes investigators snapped pictures in her office and put adhesive seals on the doors. A few days later, they replaced the seals with a lock.

The only person in the State Department who really knew what was going on was Gregory Starr, who had been briefed by the FBI in early 2013. Starr informed Raphel’s bosses about a “serious situation,” and recommended that Raphel’s Top Secret clearance be suspended.

Starr told David Wade, the chief of staff to Secretary of State John Kerry. According to Wade, Starr’s description of the case made him think the evidence against Raphel was “unimpeachable” and that the State Department could do nothing to push back. Wade informed his boss.

The next morning, agents from Diplomatic Security knocked on Raphel’s door. They took her State Department badge and BlackBerry. She was summoned to the State Department’s human-resources department and told that her employment contract, which was about to expire, wouldn’t be renewed.

Eight days later, on Oct. 30, FBI agents sent Raphel a list of personal items she would be allowed to take home. Among them: her purple briefcase, the bag of carrots and the Rubbermaid plastic container with celery sticks.

Prosecutors with the U.S. Attorney’s office wouldn’t tell her lawyers anything about the allegations. Everything, including the means by which the FBI obtained the evidence, was a national-security secret.

To keep the story out of the media, Raphel’s bosses hadn’t told her co-workers why she wouldn’t be coming back to work. Yet on Nov. 21, a story about the espionage investigation appeared on the front page of the New York Times.

That evening, Richard Hoagland, a former ambassador who worked closely with Raphel in Pakistan and Washington, met her at Bar Dupont, a popular hangout on one of Washington’s busiest traffic circles. Figuring the FBI was tailing her, Hoagland chose a table at the bar where the two of them would be easy to spot. “I wanted the FBI to see us together,” he recalled.

The next day Hoagland posted a message on his Facebook page: “Robin’s a friend of many years. We met last night for drinks. She said it’s like falling into Kafka World. People, we are a democracy with rule of law. Let’s remember every citizen is presumed innocent.”

Beth Jones worked to keep Raphel’s friends and colleagues informed. Jones figured the FBI was monitoring her office phone at the U.S. mission to the United Nations in New York, so she made her calls on Raphel’s behalf from her cellphone while walking the streets of Manhattan.

As the drama unfolded, Alexandra was in the middle of planning her wedding. She talked about postponing it—concerned that her future in-laws would think their son was marrying the daughter of a spy.

In Islamabad, the allegations were the talk of the town. Pakistani businessman Rashid Khan pulled aside Richard Olson, the U.S. ambassador, to ask him about the case against Raphel.

“Rashid, I can’t talk about it,” Olson said.

On Nov. 7, Lodhi tapped out an email to Raphel—knowing full well the FBI would likely read it. “I just wanted you to know my thoughts and prayers are with you,” she wrote. “I can think of no one more loyal to her country than you. I am sure this is a huge mistake.”

“Thanks, Maleeha,” Raphel replied cautiously five hours later. “I am in total shock of course. I know you appreciate my patriotism as I have appreciated and respected yours over the years. I am confident this will be resolved.”

After this exchange, Raphel decided to cut off communications with most of her Pakistani contacts. To keep her mind occupied, she attended seminars. At an event sponsored by the Atlantic Council, she ran into Munter, the former U.S. ambassador. Munter could see how distressed she was about the allegations and how adamantly she rebutted them.

“They’re screwing her,” he thought to himself.

PART 4 THE AFTERMATH

In the fall of 2014, the FBI began interviewing Raphel’s State Department superiors and co-workers to try to fill in the missing pieces of their investigation.

They asked Grossman why he employed her, why she traveled to Pakistan, who she met with while she was there, whether he would give her instructions on what to tell her Pakistani interlocutors during her visits and whether she reported back on her conversations.

“Yes, yes, yes, because that was her job,” Grossman told them, according to an official briefed on the investigation.

Grossman told the FBI he “trusted her to do and say the right things,” the official said.

In other interviews, the agents asked her colleagues about a series of “incidents” that seemed suspicious to the FBI. Officials briefed on the investigation said the “incidents” referred to specific communication intercepts in which Raphel discussed sensitive topics, such as coup rumors, with Lodhi and others. The FBI agents wanted to know if she was authorized to discuss these things.

State Department officials told them she may not have been specifically “instructed” to do so in every instance, but she was “authorized” to discuss anything related to U.S.-Pakistan relations if her contacts wanted to—and so long as she didn’t divulge classified information.

“Any dinner party in E-7 is going to include a discussion about what are the odds of a coup,” one of Raphel’s superiors told the agents. “It may look secret from Washington’s perspective but it’s actually pretty widely known in Pakistan.”

State Department officials said that when they spoke to the FBI agents, they had the feeling they were explaining the basics of how diplomats worked.

At times, Raphel’s colleagues pushed back—warning the FBI that their investigation risked “criminalizing diplomacy,” according to a former official who was briefed on the interviews.

In one interview, the agents asked James Dobbins, who served as SRAP from 2013 to 2014, whether it was OK for Raphel to talk to a Pakistani source about information that wasn’t restricted at the time but would later be deemed classified.

“If somebody tells you something in one conversation, you might write that up and it becomes classified,” he said. “But that doesn’t mean the next time you see them that you can’t talk about what you’d already talked about.”

Agents asked if she was authorized to discuss topics in the President’s Daily Brief—the daily gathering of the U.S. intelligence agencies’ most valuable information. State Department officials were baffled by the question because she had no access to such a sensitive document. If she discussed similar information, they told the FBI, it came from her Pakistani contacts, not from reading U.S. intelligence reports.

Added together, the interviews undercut the notion that Raphel was working on behalf of Pakistan. Two senior law enforcement officials who were involved in the case said the bureau had misconstrued her conversations with Lodhi and others, and incorrectly identified her as a spy. The bureau had not fully understood Raphel’s role within the State Department and her bosses’ expectations of her. The critical distinction, many officials said, was in how differently the FBI and the State Department operate.

“It’s cultural,” a former official said. “The FBI is very structured about communications. Agents see things as binary—on or off, authorized or unauthorized, black and white. The State Department has a bunch of informal communications channels. Things are gray. It’s just the way State is.”

In the meantime, the FBI had ignited a wider debate about how the State Department handles secrets. In 2016, several diplomats who worked closely with Raphel were questioned by the FBI for sending vaguely worded emails related to U.S. drone strikes that were found on Hillary Clinton ’s private email server when she was secretary of state. Some of Raphel’s emails were included in the trove that was reviewed by the FBI during their now-closed investigation.

In July, FBI Director James Comey decried the “security culture” within the State Department as “generally lacking in the kind of care for classified information found elsewhere in the government.”

State Department officials, in turn, said it was the FBI probe that damaged national security.

In the spring of 2015, a prosecutor in the U.S. Attorney’s Office handling the Raphel case notified Amy Jeffress, one of Raphel’s attorneys, that the Justice Department was no longer investigating her client for espionage.

That was the good news. Yet the FBI still wanted her to be prosecuted for mishandling classified information—a charge that could result in jail time.

Alexandra got married on May 23, 2015, in a ceremony in Washington that was attended by more than 250 guests, including Jilani, the Pakistani ambassador, who sat at a table with several other Pakistani friends.

Alexandra had invited Lodhi, who had taken a post as Pakistan’s ambassador to the United Nations in New York. Lodhi sent word at the last minute that she had to attend a conference in Europe.

Raphel heard nothing for months from the FBI. She had already spent about $100,000 on legal fees, which she paid by tapping into her savings, but the bills were piling up. Jones set up a legal-defense fund and 103 of Raphel’s friends and colleagues, mostly from the State Department, donated nearly $122,000.

Inside the Justice Department, prosecutors went back and forth on the merits of the case against Raphel, officials say. The most sensitive document the FBI recovered was 20 years old, and if she were charged, it could well have been routinely declassified while she awaited trial.

More importantly, the officials said, federal prosecutors tend to charge people with mishandling national secrets when they have reason to believe the suspect has in fact done worse—in part to avoid bringing spy charges that might result in having secrets aired in court.

On March 21, 2016, 17 months after the raid on her house, a U.S. prosecutor informed Jeffress the Justice Department had decided to decline prosecution.

Raphel called Jones to give her the news. “Can you believe it?” she said.

“We’re having a celebratory dinner tomorrow night,” Jones said. “Tell me who to invite.”

As Raphel and her close friends sipped Champagne, officials at the FBI and Diplomatic Security tried to come to terms with the outcome.

A senior law-enforcement official said given another chance the bureau would follow the same path again. “Clearly she was not a spy,” the official said. “But there was smoke. The FBI had to get to the bottom of it.”

Another official said that even though no charges were ever filed against Raphel, investigators were partially satisfied by the outcome. To law enforcement and intelligence officials, the loss of her government job was justified by the discovery of the documents in her house and by the signals intelligence that showed her allegedly discussing topics that the FBI considered off limits, this official said.

Raphel’s lawyer, Amy Jeffress, called it “deeply disturbing’’ that law enforcement officials “continue to make anonymous and self-serving allegations about her conduct,’’ adding that “there was no evidence she ever provided classified information to anyone without authority.’’

State Department officials now say they feel guilty about what happened. They think the FBI went off half-cocked and boxed them in by overstating the facts of the case.

Gregory Starr and other State Department officials briefed on the investigation now suspect the FBI agents wrongly assumed the information Raphel was exchanging with Lodhi and others came from classified intelligence reports, rather than from her own conversations with her contacts, according to officials.

It was a mistake, they said, to assume U.S. spy agencies had a monopoly on information in a place like Pakistan, where “secret” U.S. efforts were openly discussed in parliament, at dinner parties, and in the press.

Though the FBI probe of Raphel was dropped, Diplomatic Security has been reviewing the documents found in her basement to decide whether to cite her with a security violation. The outcome could clear the way for her to have her security clearance restored. They have yet to reach a verdict.

Over the past two years, diplomats in Pakistan and the U.S. have scaled back contacts, according to officials in both countries. U.S. diplomats say they are afraid of what the NSA and the FBI might hear about them.

“What happened to Raphel could happen to any of us,” said Ryan Crocker, one of the State Department’s most highly decorated career ambassadors. Given the empowerment of law enforcement after 9/11 and the U.S.’s growing reliance on signals intelligence in place of diplomatic reporting, he said, “we will know less and we will be less secure.”

“Look what happened to the one person who was out talking to people,” said Dan Feldman, Raphel’s former boss at State. “Does that not become a cautionary tale?”

Raphel returned to Islamabad this August. It was a personal trip. Ambassador Jilani had invited her to his son’s wedding.

To welcome her, and also to show Pakistani officials she was no longer an outcast, U.S. Ambassador David Hale hosted a dinner for Raphel in his residence. Several former ambassadors accepted the invitation, including Lodhi.

Raphel was honored by the gesture but wary of how the dinner might be perceived. She told the embassy she didn’t want any cameras present.

Dinner was called at around 8 p.m., early by Pakistan standards. The guests moved into the adjoining dining room and took their seats around the table, where Raphel, wearing a Pakistani kurta over narrow trousers, was placed directly across from Hale.

Still relatively new to Pakistan, Hale had yet to establish deep connections with many of the guests in the room. Colleagues describe him as reserved, in many ways the opposite of Raphel. After Hale delivered a gracious toast, calling Raphel one of his mentors, Raphel thanked him and thanked her old friends for their support. She didn’t mention the FBI.

At around 10 p.m., also early by Pakistan standards, Hale left the party. He told his guests he had phone calls to make to Washington. Hale declined to comment about the dinner party, citing embassy protocol.

Before the guests dispersed, Lodhi pulled Raphel aside to talk. The FBI investigation had a chilling effect on their relationship, mutual friends say. Raphel knew that her voluminous conversations with Lodhi had helped to fuel the bureau’s suspicions.

As they stood there together, apart from the other guests, Lodhi leaned in close to Raphel.

“I’m glad this is over,” she said.

In March 2016, Raphel wrote a personal letter to Secretary of State John Kerry, urging the department to do more to protect diplomats who are trying to do their jobs. She has yet to receive a response. Officials said Kerry was awaiting the outcome of the internal review of the classified documents found in Raphel’s house.

On Nov. 28, she attended a ceremony in the State Department’s seventh floor Treaty Room to mark Ambassador Olson’s retirement.

More than 100 of Olson’s colleagues, contacts and friends attended, including Beth Jones, Patterson, and Ambassador Jilani, who had supported Raphel during the investigation.

After the speeches were given and the photographs taken, Kerry and Raphel pulled away from the crowd for a private chat. It was their first face-to-face since the FBI torpedoed her diplomatic career.

Diplomatic Security had yet to restore her security clearance. Some of her friends at the State Department said they believed the FBI opposed the idea.

Kerry and Raphel stood close together for only a couple of minutes. On the sidelines of the noisy gathering, Kerry leaned over and whispered into Raphel’s ear: “I am sorry about what has happened to you.”

—Saeed Shah contributed to this article.

Write to Adam Entous and Devlin Barrett at  [email protected]