Chughtai, who in the 1990s had set up a MRI machine next door to Mahmood and knew that Mahmood and Ahmad were friendly, said he had heard rumors that Ahmad had once accompanied a nuclear scientist to see bin Laden, but had forgotten the scientist's name. And that was what the counterterrorism agent was most interested in.
"(He) called me and said, 'Dr. Chughtai, I have done more research about Zaheer than anybody else. I could do a thesis,'" Chughtai recalled. "He wanted me to send everything possible on Shifa. I faxed and faxed. One day he called and asked about Zaheer going with a nuclear scientist to see Osama. I said, 'I heard the story, don't remember the guy.' He asked if I would recognize the name. I said 'maybe.' He said 'Bashiruddin.' And that was the name I remembered."
Chughtai said the FBI agent also asked about people working in the Pakistani embassy in Washington, but he didn't recognize any names.
An FBI official confirmed that the agent met with Chughtai. but refused to discuss the investigation. The official also verified to ProPublica that the agent who talked to Chughtai worked on the same team as Sarah Linden, the FBI agent who signed the affidavit against Fai and Ahmad. The FBI requested that ProPublica not name the agent, to avoid compromising the investigation.
The FBI first questioned Fai in 2007, but seemed to step up its scrutiny in 2010.
That March, the Justice Department sent Fai a letter, telling him that the Indian press had reported that he was a Pakistani agent, and if so, he needed to register with the department as a foreign agent. Fai responded after several weeks, denying he was an agent of Pakistan.
Three months later, New York police pulled Fai over and found $35,000 in cash in his car. Fai claimed the money was from a man identified by the FBI as "Straw Donor B." After getting advice from Ahmad, the donor allegedly told the FBI that the money was from Sabir, the Brooklyn imam. But the cleric wasn't even in the U.S. when Fai was pulled over, the FBI said. In his interview with ProPublica, Sabir identified Straw Donor B as a man in his 30s named "Akif" and called him "a stupid boy." Sabir denied giving Akif money for Fai. ProPublica could not find Akif.
Despite the growing pressure, Fai kept traveling the world and kept asking the ISI for more money, the FBI said. Fai's lawyers have pointed out that Fai repeatedly chose to return to the U.S., despite knowing he was being watched.
To some, Fai's behavior indicated that he believed that he was protected.
"The ISI probably told him: 'Don't worry, you're taken care of, you're part of the tacit agreement we have with the CIA,'" said Vijay Sazawal, who is from the Indian side of Kashmir and started a rival Kashmiri group in the U.S. "He's not stupid. I have to believe he was confident he was shielded."
In February, Fai traveled to Pakistan, right about the time that U.S. and Pakistan relations were starting to fall apart. CIA operative Raymond Davis had been arrested for allegedly shooting two men in Lahore--the arrest and fallout heightened tensions between the countries.
When Fai returned home, his luggage was searched. Customs agents found what appeared to be excerpts of a court filing on Davis from the Lahore High Court. Within days, Linden, the FBI agent, visited Fai at home. She asked whether he knew anyone in the Pakistan government. Yes, he admitted. But he then suggested that none of them knew him, the FBI affidavit said.
Fai also allegedly showed Linden the court filing, which had a photocopy of a photograph of Fai on the back.
Linden testified that she e-mailed Fai on July 13, asking to meet again "to talk about the situation in Kashmir." Fai agreed.
She showed up at Fai's house after he returned from a trip to the United Kingdom, on the morning of July 18. Fai again denied working with the ISI.
That night, Fai went out to dinner with family and friends. After coming home, Fai or a family member called the police to report a suspicious car parked near Fai's driveway. FBI agents were in the car.
The next morning, Fai was arrested as he drove his wife toward the subway.
Before charges were publicly announced against Fai and Ahmad, agents fanned out across the U.S., questioning about 18 men linked to Ahmad, said Shafqat Chaudhary, who serves on the boards of Ahmad's hospital and his U.S. charity, the Society for International Help. Chaudhary, a Long Island businessman, said the FBI questioned him but declined to say what they asked. He said he wasn't involved in transferring money for Ahmad and had done nothing wrong. Chaudhary said none of the men questioned by the FBI had been arrested, as far as he knew.
Sabir said law-enforcement agents--he wasn't certain which agency they were from--also questioned him, showing him photographs of Chaudhary, Akif and Ahmad, alongside several photographs of men he didn't know. He said he had not moved money to Fai.
In a phone conversation, Ahmad said he was free and working at Shifa. "Until this case is finished, I can't discuss this," Ahmad said to a ProPublica reporter. "And it could be dangerous for you, too."
Some of Fai's supporters defended him. They pointed out that Fai was arrested the same day U.S. Secretary of State Hillary Clinton was in India, where officials had long complained about his group. They pointed out that Kromberg, the assistant U.S. attorney on the case, has been accused of anti-Muslim bias. They said they believe Fai was a victim of the chill in U.S.-Pakistan relations.
"They say that when two elephants fight, it's the grass that gets trampled," said Mirwaiz Umar Farooq, the leader of a moderate separatist group in Kashmir who always traveled with Fai when visiting the U.S. "Similarly, poor Fai has been a victim of these cross-agency wars."
At a detention hearing on July 26, Fai's lawyers indicated that they will argue that even if Fai got money from the ISI, he didn't follow their directions. "His message was always his own message," said one lawyer, Khurrum Wahid, in a press conference after the hearing. "It was never the message of the Pakistani government."
Some legal experts said the case raised questions about why the Justice Department would so aggressively pursue Fai--even asking for pretrial confinement--considering the relatively light charge. Charles Swift, a former military defense lawyer who has represented high-profile terror defendants in private practice, said he researched the registration law and could not find another case where criminal charges were pursued.
Even when the Irish Northern Aid Committee in New York was accused of being a front for the Irish Republican Army, the group was only sued civilly and eventually forced to register. A group of 10 Russian spies was charged with failing to register last year but were allowed to leave the country as part of a spy swap.
Several Kashmiris said they worried that the real victim in the case would be their struggle for self-determination.
"The Kashmir movement, as we talk about it in Washington D.C., was identified with Dr. Fai," said Mumtaz Wani, a lawyer in Washington from the Indian side of Kashmir. "And we find it's a huge setback to us. At this stage I don't feel that many in Congress will be willing to talk to us. Not even Dan Burton."
Burton and Pitts announced they would donate any campaign contributions linked to Fai and Ahmad to charity. The FBI affidavit says there's no evidence any politician knew Fai's money came from the ISI. "I was really stunned that he might be an agent, undisclosed and unregistered," Pitts said. "I was shocked."
After his arrest, Fai sat down for another interview with Linden.
This time, Fai admitted that he had been affiliated with the ISI for 15 years, and that no one on the Kashmiri American Council's board had known the group was funded by the ISI, Kromberg said at the detention hearing. Fai also allegedly wasn't just bankrolled by Pakistani spies. Instead, Kromberg said, Fai "agreed that the ISI directs him, Mr. Fai, to go to certain conferences and to report on certain people, including some that were mentioned in the criminal complaint."
Fai told ProPublica he's stopped talking to Ahmad, or anyone else in Pakistan. He said he doesn't want anyone else to get in trouble.
While under house arrest, Fai keeps working, even as he reports all his meetings to the FBI. He goes to the mosque to meet friends. He edits a new 54-page paper on Kashmir, focusing on topics such as the U.N. resolution from 1949 and the visit of the imam of Kaaba in 1980. He sends out emails to the Kashmiri American Council's mailing list, saying he will keep fighting for Kashmiris to decide their future.
"God willing!" he wrote in one. "I will continue to do that in days, weeks, months and years to come."
This article also appears at ProPublica.org