It's not hard to see why the US government would view Naji as an ideal informant. He is religious, conservative, and speaks English and Arabic. He's calm under pressure. He had crisscrossed the globe as a volunteer escort for refugees being resettled through the International Organization for Migration. When he traveled, he went to mosques and counted on the hospitality of strangers to find a bed for the night, and through this he had made connections with dozens of other religious Muslim men around the world.

This is precisely the kind of community that the FBI is trying to track and infiltrate. The bureau's network of paid informants has expanded rapidly since 9/11, and now includes more than 15,000, rivaling the scale of the J. Edgar Hoover era. A guy like Naji—an expatriate working in countries where terrorists operate—would be a real catch.

But to someone not facing criminal charges, the FBI doesn't have much to offer by way of enticement. "The problem for many American Muslims who have been approached by the FBI to become informants is that they aren't involved in criminal conspiracies and don't have relationships with criminals," says Mike German, an ex-FBI agent who now works for the Brennan Center for Justice at New York University. "Instead, they are being asked to spy broadly against their religious community. That creates a conundrum because the person may be perfectly willing to help the FBI fight terrorism but simply has no information to provide."

Naji told Roberts he was planning to move to Juba, where his mother had taken a job with a company called Management Systems International that did work for USAID. He hoped to launch a business there selling rugged laptops. "We could use you there, too," Roberts said.

"No, man," Naji replied. Spying was "not something I want to play around with," especially in a country like Sudan. "This is Africa. There's no law for me here."

Six weeks after the raid, the Mansour family headed to the Nairobi airport to fly to Uganda for a visit with Naji's ex-wife and their children. When Naji handed his passport to a security officer, she glanced at her computer screen, stared at him, and asked, "What did you do?" Kenyan security officers detained the family for several hours, releasing them just before their flight took off.

When the family returned five days later, Kenyan airport police questioned Naji again. "The deputy immigration officer said, 'We have nothing wrong with you, but we have a directive not to let you in,'" Naji recalled. Soon, Fogarty and Jones showed up at the airport. The FBI agent reiterated the US government's desire that Naji become an informant. Naji once again declined.

He spent three nights at the airport, and when it became clear that he would not be allowed to enter Kenya, Nasreen brought him some clothes and his laptop samples and said goodbye. Then Naji boarded a plane to go stay with his mother in Juba. There, he buried himself in building his laptop business. "We kept thinking things were going to blow over," Sandra said.

In late June 2009, Sandra took a business trip to Kenya, and stopped by the US Embassy to get more pages added to her passport, for all the visas needed for her international travels. She was told there was a "hit" on her passport that needed to be cleared in Washington. A few days later, she was informed her passport would be released if she'd meet with the FBI first. So on Monday, June 29, Sandra sat down with FBI agent Mike Jones. "He asked, 'Where's Naji now?'" she recalled. "I said, 'He's with me in Juba.'"

The next morning, June 30, Naji and Nasreen—who had come to visit her husband in Juba while Sandra was in Nairobi looking after their children—were about to go out for breakfast when they noticed a man peering through the window. Naji opened the door to find two men in suits, sweating in the heat, with guns on their hips. "One of them looked like African James Bond," Naji told me. "And I say, 'Yes, hello?' And they're like, 'Naji Mansour?' and I'm like, 'Yes.' And they just came in." The agents of the South Sudan Security Bureau asked Naji to bring Nasreen out, and then they took the couple's phones and laptops and hustled them into separate unmarked cars.

When I asked the FBI about why Naji and Nasreen were arrested a day after Sandra told Jones of Naji's whereabouts, a spokeswoman told me in an email that the timing "is, in fact coincidence." But there are indications that it may not have been. "Sandra, I'm not supposed to be telling you this, but this is coming from your people," Sandra says a top Sudanese official told her. A former US diplomat who was stationed in Juba at the time told me that US officials there spoke openly of Naji's detainment and said he would be freed if he cooperated with the FBI.

The agents took Naji and Nasreen to the National Intelligence building, where Naji was placed in a basement cell; later, he heard Nasreen sobbing. One of the guards was trying to remove her headscarf—most South Sudanese are not Muslim—but she prevailed. Then the lights went out. Nasreen was still whimpering in a cell down the hall.

In the days that followed, the couple was questioned about their intentions in the country, whether they had ties to terrorism, and the contents of Naji's laptops. One of them contained materials similar to those that had raised eyebrows in Kenya. Nasreen was finally freed after eight days and put on a flight back to Nairobi. No charges were ever filed, nor was she given any reason for her detention.

The weekend after Nasreen's release, guards escorted Naji into an interrogation room. Soon, a blond State Department official entered.

"Do you remember Mike Jones—you met him in Nairobi?" she asked.

"Yeah," Naji replied.

"Would you be willing to see him?" the diplomat inquired. That was fine by him, Naji said, and to his surprise Jones and another FBI agent, Peter Smith (whose real name also has been withheld at the FBI's request), strolled in moments later. Smith said he believed that Naji had done nothing wrong and wasn't involved with terrorism, but told him that the FBI needed Naji to tell them something useful so they could advocate on his behalf with the Sudanese. "Quid pro quo, Naji. Quid pro quo," Jones chimed in.

"Every time I try to cooperate with the FBI, I get deeper into shit. I'm a citizen. They're supposed to have my back, and it's the exact opposite."

Naji racked his brain. Then he remembered that Muhammad, the guy who had arranged for Berjawi and Sakr to stay with him, had once called his office phone in Dubai—a number that very few people called. Perhaps the FBI could pull the phone records and locate Muhammad. But Jones was not interested in Muhammad. He wanted to know about Omar, Nasreen's distant cousin—the one who'd later be charged in the Uganda World Cup bombings. Naji said he didn't think Omar was the "type" to join Al Qaeda, but Jones didn't seem to buy it. "All right, Naji, good luck," the FBI agent said. "I hope everything works out for you, buddy."

Then, 37 days after he'd been arrested and three weeks after his conversation with the FBI, Naji was brought upstairs again. A Sudanese officer told him he was free to go, so long as he stayed in the country for the next 30 days and didn't talk to the media.

After his release, the director of South Sudan's Security Bureau penned a memo to the local minister of internal affairs briefing him on Naji's case. "The accused has been very much willing to know in-depth about Terrorism and Islamic Jihad," he wrote in the document, which was obtained by Mother Jones. "Thus, Mr. Naji is believed to have much interest in Terrorism activities, in fundamentalism and Islamic teachings. Whether that could lead to joining such activities or help in one way or another he will just remain a suspect that would require trailing."

A month later, Naji moved to Khartoum, the capital of Sudan, where his late father's family had lived. Nasreen and their children later joined him there. He began to think his problems were over. Then, in October 2009, Jones got in touch. "I am heading back to Africa in the near future," he wrote in an email. "I'd be willing to stop by area, or Khartoum, and meet if you have the time." Naji replied that he wanted to talk on the phone before committing. He planned to tape their conversation.

When Jones called a month later, Naji turned on his phone's recording app and told the agent that he believed US officials had ordered his detention. (Clips of the conversation follow; you can listen to the entire recording and read a transcript here.)

"We had 100 percent nothing to do with that," Jones responded, according to a copy of the recording that Naji gave me. "It runs counter to everything that we do and that we stand for."

"I just want normalcy for my family," Naji said. "'Cause I think they deserve it. 'Cause it's been a screwed-up year, let me tell you." Jones pressed for a meeting, and they agreed to talk again the next morning.

Naji recorded their subsequent conversation, too. This time Peter Smith was on the line with Jones, and the collegial tone of their previous interactions was gone. The agents again asked for a meeting, but Naji declined. Ever since he had first told his story to US officials, he said, his life had been thrown into chaos. "There's scrutiny on your mom," Jones finally said. "...That's not going to go away unless we sit down and get down to business."

Smith jumped in, telling Naji that if he refused, "a series of events is going to be put into motion. And once you put it into motion, honestly I, I'm out of it. I honestly do not care. I'm going home, you know, I got a vacation to plan. My life goes on. Yours might change. And it's not going to, it might not be necessarily to your liking." He added: "I'm telling you, you might get hit by a car—that is not a threat. That is a solid piece of advice. But you don't want to take it."

(The FBI refused to comment on the bureau's attempt to recruit Naji as an informant, nor would it comment on his taped conversations with Jones and Smith or whether any misconduct on their part had occurred.)

Four days later, on November 17, a State Department security officer visited the offices of Management Systems International in Juba. Sandra was fired the same day—less than a week after the company had renewed her contract for another year. She was told her position had been eliminated, but MSI posted the same job a month later. Stefanie Frease, one of Sandra's supervisors, told me the dismissal came at the behest of the US government.

"We all thought she was blackballed," said Inez Andrews, a former foreign-service officer working in the US compound in Juba at the time. "It's awful she hasn't been able to clear this up, that she's being held hostage to a system that was trying to extract information."

In a statement, USAID maintained that "decisions regarding the termination of employees...are ultimately made and executed by contractors themselves." And an FBI spokeswoman said the bureau "made no recommendations in regards to Sandra Mansour's employment status."

But Sandra's ordeal wasn't over. When she tried to return to her home in Nairobi in 2011, she was blocked from entering the country, just as Naji had been. An immigration official told her, she recalled, "If the Americans don't want you here, you ain't coming in." She was finally allowed entry to Kenya last December, when American nationals were evacuated there after South Sudan descended into violence.

Other members of Naji's family have been targeted, too. In 2011, Naji's sister, Tahani, was detained at the Nairobi airport for three days. "I've heard, 'It's your people'"—that the US is behind her family's troubles with customs officials—"more times than I can count," she told me. "I go to airports now and there's this constant sense of trepidation. Am I gonna make it? Am I gonna get locked up again?"

"As a family we have always been mobile and traveling our whole lives, and as a result completely took it for granted," she told me. "The removal of the liberty to travel was crippling."

One of Naji's brothers says he is frequently questioned about Naji when he crosses an international border. The other, a Marine veteran based in Virginia, was visited by members of the Navy's criminal investigative service, who grilled him about Naji. The FBI even interviewed Naji's uncle and aging grandmother in Rhode Island in 2009.

"They didn't get to me, so they had to target my family," says Naji.

On September 21, 2013, members of al-Shabaab, armed with assault rifles and grenades, stormed the Westgate, the upscale mall that Bilal el-Berjawi and Mohamed Gamal Sakr had allegedly plotted to bomb four years earlier. Over the next three days, at least 72 people (including the attackers) were killed and the mall was almost entirely destroyed.

I had just left Nairobi—where I had visited Tahani at the Mansour family's home, just a few miles from the mall—the day before. As the news broke, I was sipping white tea with Naji in the lobby of the Acropole Hotel, a Khartoum landmark with a Raiders of the Lost Ark vibe and a cartoonishly large safe in its office. The hotel's prime clientele are foreign archaeologists (Sudan has more pyramids than Egypt); it's also a popular haunt for journalists, as the bumper stickers—CNN, BBC, CBC—on the lobby window attest.

Naji was skinny and 5-foot-7. He had close-cropped black hair with a sprinkling of gray, stylish glasses, and a mustacheless beard that he absentmindedly stroked when he grew sad or worried. He spoke quietly and slowly, telling me about his passion for organic food and his interest in "open-source ecology," in which people build their own tractors and plows from plans available on the internet.

Sudan, Naji told me, had become his prison. He felt trapped and helpless. He was no longer welcome in Kenya, and he feared what might happen if he set foot outside Sudan, believing he might be detained—and possibly tortured—at the behest of the US government. The experience "made me scared of traveling," Naji said. "What happens if I go to a US-friendly country or pass through a US-friendly country?"

The older two of his and Nasreen's four children now live with his mother-in-law in Nairobi (it has better schools than Khartoum), where he cannot visit them. He hasn't seen his son and daughter from his first marriage in three years. And Naji's lifelong ambition—to travel the world with his kids, "doing all the stuff with my children that my father did with me"—is blocked by fear.

Over and over during my time in Khartoum, Naji assured me that he had no ties to terrorism. I asked him about the terrorism-related files that had been found on his computer and what had kept him from following his interest in jihad down a path toward violence, as has been the case with some other conservative Muslims who have immersed themselves in extremist dogma online. "Knowledge" of Islam, he replied, explaining that he has had a long-standing "intellectual" interest in jihad and political Islam. I pressed Naji on whether he thought killing civilians was justified in certain situations. "What happened at Westgate is forbidden," he told me. "Am I a sleeper cell? I like to sleep a lot!"

In fact, it was a notorious act of terrorism that first prompted Naji's curiosity about jihad—Al Qaeda's 1998 bombing of the US Embassy in Nairobi. Among the 213 people killed in the blast was his sister's best friend, Jay Bartley, who liked to shoot hoops with Naji and his brothers. Bartley's father, Julian, the consul general, was also killed in the attack.

"The following days were a haze," Tahani told me. "I don't think I ate anything other than coffee for three days. I burned a huge chunk of my hair off with the hair dryer just in a daze." Naji, then 22, saw his sister's despair. Yet when he went to the mosque, some of the men there spoke of the attack as a legitimate act of jihad, Naji remembered. "I honestly had no idea what to think," he said. "I became very curious about how something like that could be justified under Islam."

When Naji moved to London in 1999, he fell in with a group of conservative Pakistani men. Once drawn to secular pan-Africanism, he became more devout and enthusiastic about Islam as a political solution to the world's problems. "I started learning that Islamic systems were behind some of the greatest empires," he said. He educated himself about the structure of an Islamic state—how banking and finance would be conducted, how the poor would be cared for. "'Oh wow,' I thought, 'something other than democratic socialism and capitalism'—it was very appealing to me, liberating."

Tahani didn't view her brother's increasing interest in political Islam and jihad as unusual, even in light of what had happened to the Bartleys. "He was totally open about it," she told me. Jihad "was just the next topic" for Naji. "He really takes it upon himself to properly look into things through multiple sources." She told me her brother had once been fascinated by Sufism, Islam's more mystical branch. "Naji's approach to the whole jihad thing was similar to that. There was an enigma about it and he wanted to be informed. That's what he does—he teaches himself."

As we watched Kenyan police and military units respond to the mall attack, Naji called his mother-in-law, who works in a hair salon near the Westgate. She told him that her building had been evacuated and she had fallen running away, but she and the kids were fine. Then he rolled his prayer mat out on the hotel balcony and prayed. Later we took an ancient minibus to Omdurman, Khartoum's sister city across the Nile, and sat on the sagging couches in Naji's apartment and talked until the muezzin sang the sunrise call to prayer from the minaret across the street.

"Even if I was guilty, there's a process," he told me.

Though he spent much of his life abroad, Naji had never doubted his rights as an American citizen. But the experience with the FBI had made him deeply distrustful of his government. "Every time I try to cooperate with the FBI, I get deeper into shit. I'm a citizen. They're supposed to have my back, and it's the exact opposite. You shouldn't expect this from the beacon of democracy."

On my last day in Khartoum, Naji and Sandra picked me up at the Acropole. We drove for 30 minutes to the outskirts of the city, where the US Embassy complex sits on a desolate road near a turn in the Blue Nile. Naji needed to renew his passport. He was nervous—he had told Nasreen that if he didn't return within two hours, she should notify the press and local authorities. A security officer took our phones, and then we followed a covered walkway that cut across the bright green lawn.

We stepped into a scene that would not have been out of place in a municipal building in Dayton, Ohio. It was just before 8:15 a.m. and a television mounted on the wall was tuned to the Armed Forces Network, which was showing The Doctors. Five numbered windows lined the wall. A table was covered with old magazines, and official portraits of Barack Obama, Joe Biden, and John Kerry peered down from the wall. Soon, a disembodied voice asked Naji to report to window one. He handed in his form and his passport. As we waited, 10 or 12 other people renewing passports came and went. Finally, after about an hour, a voice announced over a loudspeaker, "Excuse me, Mr. Mansour? Can you go to window number six?" There was no window, only a soundproof door, marked "INTERVIEW ROOM."

Inside, a window looked through to another room, but its shades were drawn. After a few minutes, the shades rose and two State Department officials were on the other side: Chris McVay, an assistant regional security officer at the embassy, and a woman who introduced herself as Amelia Sanders, the second secretary for regional, political, and economic affairs. They didn't mention any of Naji's previous troubles, although they brought up his time in Juba and travels throughout Africa. The diplomats said they were interested in hearing Naji's thoughts about the countries he had visited. Before they let him go to collect his passport, Sanders asked if perhaps they could meet again sometime soon.

This story was supported by the Fund for Investigative Journalism.