PESHAWAR, PakistanIn his native Pakistan, Dr. Shakil Afridi is considered a traitor by many people for helping the Central Intelligence Agency track down and kill Osama bin Laden. In the United States, he is hailed as a hero.

In global health circles, his story is a cautionary tale about the consequences that can spiral out of control when health professionals get too close to intelligence operations.

More than three years after U.S. Navy SEALs raided bin Laden's compound in Abbottabad, Pakistan, it remains unclear whether Afridi knew he was working for the CIA when he led a hepatitis B vaccination campaign that helped U.S. agents learn where bin Laden was hiding.

Afridi's wife and his current lawyer, Qamar Nadeem Afridi, who is the doctor's cousin, say that he didn't know of the CIA connection, and U.S. intelligence specialists say that even if he did know, Afridi almost certainly had no idea that the man whose location he helped to identify was the world's most wanted terrorist.

The exposure of the CIA's role in the vaccination effort landed Afridi in a Pakistani prison and, health officials say, became a major setback in the efforts to vaccinate Pakistanis against another highly contagious disease: polio. Concerted vaccination efforts had come close to eliminating the crippling virus in the early 2000s, but it had flared up again in 2012 in the cities of Karachi and Peshawar and in the tribal belt along the Afghan border.

The blowback from the raid may well have extended beyond Pakistan. Health specialists say the suspicion, anger, and violence that some Pakistanis and Taliban militants directed at health care workers after news leaked about the CIA-orchestrated vaccination campaign may have contributed to the spread of polio in Pakistan and war-torn parts of Syria and Iraq.

Today, Afridi is in solitary confinement at Peshawar Central Prison, a fortified red-brick remnant of Britain's colonial rule that is crammed with more than 2,000 inmates, ranging from petty thieves to Taliban assassins.

Afridi's Story

To shed light on this central yet elusive figure in what has evolved into a dangerous regional health crisis, National Geographic, with support from the Pulitzer Center on Crisis Reporting, sent reporters to Islamabad and Peshawar to interview members of the Afridi family, his lawyer, Pakistani officials, and local health workers. In Washington, D.C., they interviewed U.S. government officials and members of the intelligence community.

National Geographic also examined previously classified documents on Afridi's role in the CIA's operation. Among the most revealing of these is a report written by the Abbottabad Commission, an independent inquiry ordered by Pakistan's federal government in Islamabad to examine how the Americans found out where bin Laden was hiding while Pakistan's national security agencies apparently remained unaware.

Scathing in its criticism of Pakistani army and intelligence officials, the report was suppressed by the Islamabad government until a copy was leaked to the media last year.

The picture of Afridi that emerges from the Abbottabad Commission report, and from interviews with those who know him, depict a perfect potential recruit for the CIA.

Shakil Afridi graduated from Khyber Medical College in Peshawar in 1990. He went on to serve as a senior health official of Khyber Pakhtunkhwa Province, along the mountainous Afghan border, where Taliban and al Qaeda fighters found a stronghold among fiercely independent Pashtun tribes.

In 2008, Afridi, who had become part-owner of a private clinic near the Khyber Pass, was kidnapped by Mangal Bagh, a former bus driver turned commander of a Pakistani militant group called Lashkar-e-Islam, which openly boasted about grabbing the doctor.

The group initially demanded a ransom of 1.5 million rupees (about $15,000 U.S.), but the kidnappers eventually settled for $10,000. Afridi's wife had to sell her wedding jewelry to raise the cash, and the doctor was eventually released.

Shaken by his kidnapping, Afridi decided to leave Pakistan with his wife and three children for the United States, where they had family. They secured visas and moved to California for a time but returned to Pakistan because, as Afridi told the Abbottabad Commission, the American way of life did not suit him and he did not want his daughter to grow up with Western values. Moreover, Afridi was not licensed to practice medicine in the United States, and he was loath to do menial jobs.

By late 2009, Afridi had returned to Pakistan, where he attended a seminar for health officers and coordinators hosted by Save the Children, an international charity dedicated to children's health issues, which had been operating in the country for more than 30 years. The United States Agency for International Development (USAID) had partnered with Save the Children to inoculate children against various diseases throughout Pakistan.

According to the Abbottabad report, Afridi claims he was approached by an Australian from Save the Children who then introduced him to "Kate," an American woman who operated the agency's vaccination campaigns in the tribal region along the Afghan border.

Afridi told Pakistani investigators that over the course of their meetings throughout 2010, he provided Kate with information about his captor, Mangal Bagh, and the drug lords who smuggle opium and hashish through the Khyber Pass.

But he told a different story to his earlier interrogators at Pakistan's Inter-Services Intelligence (ISI), whose questioning techniques are seldom gentle. To them, he allegedly claimed that he was recruited by the CIA through USAID.

The Waziristan Apartment

The Abbottabad report says that in January 2011, four months before the raid on bin Laden's compound, Kate asked Afridi to launch a hepatitis B vaccination campaign in areas near Abbottabad, a military garrison town about 100 miles (160 kilometers) west of Peshawar.

This campaign encompassed Bilal Town, a wealthy suburb where a three-story white house surrounded by 20-foot-high (6-meter) walls drew the curiosity of neighbors. Locals had nicknamed it the "Waziristan Kothi" (the Waziristan Apartment) because its inhabitants kept to themselves and were widely believed to have fled from a blood feud in their native Waziristan, a common occurrence among the tribes along the Afghan border.

By then, a disgruntled former Pakistani army officer had tipped off the CIA that a prominent al Qaeda militant might be living behind the towering walls of the Waziristan Kothi.

For U.S. forces, launching a raid on the suspected hideout held many risks. The Pakistani military could shoot down the helicopters or attack the Navy SEALs on the ground. The possibility of a bombing run was ruled out early because there would be no way of collecting a DNA sample from the rubble to prove that bin Laden had been killed.

"It doesn't take a whole lot of imagination to figure out that the operation could go disastrously wrong," says Robert Grenier, a former director of counterterrorism for the CIA. "And then you find out it wasn't bin Laden, just some crazy uncle they kept in the attic."

Grenier says that the CIA's Islamabad station was undoubtedly under "tremendous pressure" from their bosses at the agency's Langley, Virginia, headquarters to confirm the identify of the mystery man pacing the villa's top floor.

At the time, the ploy of staging a vaccination campaign to gain entry to the compound might have seemed fairly risk-free. The decision to enlist Afridi was probably made by the CIA station chief in Islamabad and was passed on to the Counterterrorism Center back in Langley.

"The driving force for this operation would have been counterterrorism," says Grenier. "They know a lot about terrorists and terrorism, but they don't always know the context in which something is happening—or the unforeseen consequences of failure."

In this case, that meant knowing, or caring, that even before the Abbottabad raid, considerable hostility to vaccination campaigns persisted in the tribal areas, where some village imams had claimed that the polio vaccines were part of a Western plot to sterilize Pakistani Muslims.

Banging on the Gate

Save the Children has denied working with Afridi and the CIA. Regardless, the campaign that Afridi ran was in fact authentic. Banners and posters announcing the immunizations were plastered around town. Women from the Lady Health Workers, an organization tasked with immunizing children and women across Pakistan, went door-to-door administering genuine doses of hepatitis vaccine.

Afridi told Pakistani investigators that his payment of 1.3 million rupees (roughly $12,750 U.S.) was directed to his personal bank account. That was not unusual. In many developing nations, aid agencies use a variety of roundabout bookkeeping methods to circumvent local bureaucracies.

More unusual was Kate's insistence that Afridi hide in the back of her vehicle to avoid being seen with her in public whenever they drove to their meetings at a USAID warehouse.

In April 2011, Afridi was told by "Sue," a second American woman whom he says he met through Save the Children, that he should monitor the work himself. On either April 20 or 21, Afridi, accompanied by a local female health worker, banged on the heavy metal gate of Waziristan Kothi.

In his testimony to Pakistani interrogators, Afridi expressed no suspicions that his employer had another motive for launching a vaccination campaign in Abbottabad beyond health care and research. In any event, says former CIA officer Grenier, it is doubtful that the CIA would have confided to Afridi that their intended target was bin Laden. "The agency would have been very reluctant to tell him," he says.

The CIA's plan was for Afridi to herd out the children from the villa for vaccination, according to testimony by women from the Lady Health Workers who participated in the campaign.

Afridi would collect the spent vaccination needles, which his handlers would then send to the CIA to determine if the DNA on them closely resembled bin Laden's DNA. If the samples matched, it would prove the children were related to him and strongly suggest that it was the al Qaeda leader who was hiding on the upper floors.

In that regard, Afridi failed.

When he and the health worker arrived at the Waziristan Kothi, he was told by a woman answering the gate that none of the residents were home. Afridi insisted on speaking with the owner of the house and was able to obtain a telephone number belonging to "Ibrahim Saeed Ahmed," who was said to live in the compound. This turned out to be a vital piece of information for Sue, Afridi's CIA handler.

Thirty-Eight Minutes

Previously, the CIA had learned from another source that a man named Ibrahim Saeed Ahmed was bin Laden's trusted courier. The intercepts from the phone number Afridi provided—while not as good as the children's DNA—were considered a crucial piece of the evidence presented to the White House in support of green-lighting the highly risky raid on the compound.

It is doubtful, intelligence specialists say, that the White House would have been consulted during the intelligence-gathering phase of the operation or that President Barack Obama's national security advisers would have been drawn into a debate over the possible repercussions of having spies use health workers as a cover.

Starting a little after midnight on May 2, 2011, SEAL Team Six spent a total of 38 minutes on the ground in Abbottabad, ending the ten-year manhunt for Osama bin Laden.

While the Western world celebrated the killing of the world's most wanted man, Pakistani politicians and generals were fuming. The U.S. hadn't consulted them about the raid, which they saw as a violation of their national sovereignty. And the discovery that bin Laden was hiding so close to Pakistani military installations gave rise to speculation that Pakistan's spy agency, the ISI, either was incompetent in tracking bin Laden or complicit in his hiding.

ISI agents began interrogating anyone who had approached the bin Laden compound in the weeks before the U.S. raid. It wasn't long before they learned about Afridi's vaccination drive. The ISI says it arrested Afridi on May 23, 2011, at Torkham, a main border crossing, as the doctor was trying to flee into Afghanistan.

Afridi's wife disputes this version. She says he had no intention of fleeing and was picked up at a local market near Peshawar. According to the Abbottabad Commission, Afridi said he had every intention of finishing the second round of the hepatitis vaccination drive in Abbottabad.

The CIA had ample time to pull Afridi and his family out of Pakistan. If the family members had wanted to leave, they already had U.S. visas, according to Afridi's lawyer.

In the event that a local CIA operative is compromised and faces possible arrest, or worse, it is the agency's standard practice to urge him or her to leave the country. Says Grenier, who ran a network of informants in his various overseas postings, which included a stint as Islamabad station chief, "These [informants] usually have a strong instinct of self-preservation, but you sometimes find a few who have a preternatural confidence that they can get away with anything." He adds: "Those are the ones you really have to watch out for."

When Afridi was arrested three weeks after the raid, he claimed he did not realize what role he had played until after his arrest.

Word Gets Out

Saeed Shah, a Pakistani journalist reporting for the McClatchy newspaper chain, first broke the story of the CIA's use of the vaccination program.

"The U.S. administration tried to stop me [from] publishing the story, both the CIA and the State Department, by approaching my editors at McClatchy, and also by appealing to me directly by telling me that it would put Afridi's life at risk," Shah told PolitiFact, the politics fact-checking organization.

Save the Children also was caught up in the sweep.

Its six foreign staffers were expelled from Pakistan. The charity's country director, David Wright, gave a statement to the Abbottabad Commission saying that one staffer briefly had met Afridi at a health conference in Peshawar but that was the charity's sole contact with the doctor.

Wright said he was "outraged by this misuse of our name … that a lifesaving activity such as a vaccination campaign would be used for nonmedical or nonhumanitarian purposes."

The Abbottabad commissioners concluded that Save the Children lacked "the internal mechanisms" to detect that it had been "infiltrated" by the CIA.

The CIA has strict regulations that prohibit it from using American companies and entities as fronts and must seek the company's consent before it plants an agent in its midst. One ex-CIA agent said that no such restrictions apply to foreign companies, which are considered fair game for infiltration. However, the Pakistani branch of Save the Children was run through the U.S. office.

Former staffers of the charity say they doubt Afridi's assertions that Save the Children was used as a cover for the CIA. The likeliest explanation, they say, is that after the initial introduction, there was no direct link between the organization and Afridi's CIA handlers.

National Geographic made several attempts to seek further clarification from Save the Children about its alleged ties to Afridi, but the charity declined to comment.

The CIA's manipulation of the vaccination campaign angered public health experts in the U.S. who worried that it might cast a pall of suspicion over aid workers in other countries too. In January 2013, the deans of 12 top public health schools wrote a letter to the Obama administration demanding that it cease using health workers in covert operations, citing the resurgence of polio in Pakistan.

The CIA complied. In August 2013, the director of the CIA told the agency to "make no operational use of vaccination programs, which includes vaccination workers." And then in May last year, Lisa Monaco, a counterterrorism and homeland security adviser to the president, wrote: "Similarly, the Agency will not seek to obtain or exploit DNA or other genetic material acquired through such programs. This CIA policy applies worldwide and to U.S. and non-U.S. persons alike."

Before the Tribunal

After his arrest, Afridi was interrogated repeatedly by the ISI. He was moved from Peshawar to Abbottabad and then on to Islamabad, where he was held in solitary confinement for seven days. Then he was returned to Peshawar. At one point, Afridi told his lawyer, he was handcuffed and tossed into a cell with a prisoner from the same extremist militia that had kidnapped him.

Meanwhile, in Washington, D.C., the wheels began to turn to try to secure Afridi's freedom. In July 2011, acting CIA Director Michael Morell and ISI Chief Lieutenant General Ahmed Shuja Pasha discussed releasing Afridi. But no agreement was reached.

In defense of using Afridi, a senior U.S. counterterrorism official said, "The vaccination efforts carried out under Dr. Afridi's auspices were both limited and, more importantly, real." He added, "The idea that these were in any way 'fake' is simply mistaken. Many Pakistani children received vaccinations, and if the effort had not been interrupted by the arrest of the doctor, they would have been fully immunized."

In May 2012, a Pakistani tribal court decided not to charge Afridi with treason and instead fined him $3,100 and sentenced him to 33 years in prison for providing financial assistance to Lashkar-e-Islam, the same militia that had held him hostage in 2008.

This "financial assistance" was the ransom his family had been forced to pay after the group kidnapped him. Outlawed groups like Lashkar and the Pakistani Taliban run many extortion and kidnapping rackets, yet this was one of the rare instances in which someone went to jail for paying off their captors.

Afridi has appealed the tribunal's decision, and after reviewing the case, an official of the Frontier Crimes Regulation has reduced his sentence by ten years. Dissatisfied with a mere review, Afridi's lawyer is trying to get a retrial so that his sentence can be overturned. They say they are struggling to get government documents needed for their case.

U.S. Response to Afridi's Plight

In Washington, Republicans have been vocal in criticizing Pakistan's treatment of Afridi. At a congressional hearing on U.S. foreign assistance last April, Republicans questioned U.S. funding for Pakistan, which amounts to $882 million annually.

Representative Dana Rohrabacher reiterated to members of the House Committee on Foreign Affairs, "Pakistan arrested and is still holding and brutalizing Dr. Afridi, who helped us identify and locate Osama bin Laden, who was responsible for slaughtering 3,000 Americans."

The U.S. State Department continues to lobby for Afridi's release. In response to questions from National Geographic, the State Department issued a statement: "Our position on Dr. Afridi has long been clear: We believe his treatment is both unjust and unwarranted."

It added: "We regret that he was convicted and the severity of his sentence. We continue to believe the prosecution and conviction of Dr. Afridi sends exactly the wrong message about the importance of this shared interest and hope for a disposition in [this] case that reflects that bringing Osama bin Laden to justice was clearly in Pakistan's interests."

Meanwhile, the Obama administration is exploring other avenues. A U.S. government official, who asked not to be identified because the official was not authorized to speak publicly, referred to press reports that Afridi could be swapped for Aafia Siddiqui, a female Pakistani neurologist with ties to al Qaeda. She is serving an 86-year sentence in a U.S. prison for attacking personnel from the Federal Bureau of Investigation and the military in Afghanistan.

Freeing Siddiqui is a pressing cause for Islamists, including many outside of Pakistan. The Islamic State, the radical Islamic militant organization also known as ISIS, reportedly offered to exchange American journalist James Foley for her. In August, the group beheaded Foley.

This government official said that for now, an exchange is not something the U.S. government is "willing to entertain."

Meanwhile, the Taliban have a death warrant out for Afridi. "He is now top of our list," Pakistani Taliban spokesman Ehsanullah Ehsan told CNN. "We will cut him into pieces when and where we manage to reach him."

Tuesday: Part 3—The plight of a Pakistani polio worker

This series was reported in cooperation with the Investigative Reporting Program at the University of California, Berkeley, Graduate School of Journalism and supported in part with a grant from the Pulitzer Center on Crisis Reporting. Additional reporting on the polio series was done by Sarah Dadouch, Jake R. Nichol, James Reddick, and Sally Schilling.