The men were ready. They knew the woman who would be joining them for the week was a high-profile Al Qaeda operative. They'd been told she should be treated with the utmost respect. She would arrive in Liberia's bustling capital, Monrovia, on a plane from Quetta, Pakistan. She was to be driven to the safe house, the Hotel Boulevard, where other Al Qaeda figures had stayed, and taken good care of until the deal was done.

The trip from the airport was a hot hour long, and the woman spoke in English to the driver on the way. The driver, who would later become the chief informant in a United Nations-led investigation, described her as a quiet Islamic woman who wore a traditional headscarf and kept mostly to herself. She spent the week holed up in her room, making trips into town for small errands.

About a week after her arrival, the woman left Monrovia as quietly as she had entered, but now she had what she had come for: a large parcel containing gems from Africa's illegal diamond trade. They would be used as a convenient, hard-to-trace way of funding Al Qaeda's global terror operations. It was mid-June 2001, three months before September 11.

The men never saw the woman again in person. But earlier this year, one of them says, he saw two photographs of her. At a news conference in May, Attorney General John Ashcroft and FBI Director Robert Mueller III announced that the FBI was looking for seven people with suspected ties to Al Qaeda. MIT graduate and former Boston resident Aafia Siddiqui was the only woman on the list. After the photos of her appeared on television, the informant picked up the phone and dialed investigators at the Special Court for Sierra Leone, which is examining Africa's illegal diamond trade. The informant was convinced that the woman in the photographs was the woman who had come to Liberia.

Now imagine this: The woman in the photographs, Aafia Siddiqui, the same week, mid-June, 2001. She is a 29-year-old mother of two, consumed, like other Boston moms who volunteer or work outside the home, with the minutiae of everyday life. A deeply religious woman, she picks up Korans from a local mosque and distributes them to inmates in area prisons. She hosts play groups in her apartment on the 20th floor of the Back Bay Manor in Roxbury. She takes her sister Fowzia's child into her care while Fowzia finishes a fellowship in neurology at Brigham and Women's Hospital. She does the grocery shopping and prepares meals for her children and husband, an anesthesiologist at Brigham and Women's.

This is what Aafia Siddiqui's family says she was really doing during the summer of 2001. Not brokering diamond deals for Al Qaeda with murderous brutes from the killing fields of Africa, but hosting play groups in her apartment. "Aafia Siddiqui was here in June 2001," says the family's attorney, Elaine Whitfield Sharp. "And I can prove it."

Sharp is best known as one of the lawyers who defended Louise Woodward, the English nanny found guilty of shaking infant Matthew Eappen to death in 1997. If she can prove Siddiqui wasn't in Liberia that week, she'll damage one of the most puzzling cases of alleged terrorism to emerge from the ashes of 9/11. The claim that Siddiqui was involved in diamond trading is another in a series of sometimes surprising, sometimes vague accusations by government officials. In Siddiqui's case, the allegations have been further clouded by the often inaccurate, even hyperbolic descriptions of her by the media.

To those who knew her, Aafia Siddiqui was a kind, quiet woman living the normal life of a Pakistani expat in Boston. To the FBI, which displayed her photograph at that press conference in May, she was a suspected terrorist with ties to a chief mastermind of 9/11 -- and the knowledge, skills, and intention to continue Al Qaeda's terror war in the United States and abroad. Could one woman embody such diametrically opposed identities? Who is the real Aafia Siddiqui? And where has she gone?

Born in Karachi, Pakistan, on March 2, 1972, Aafia was one of three children of Mohammad Siddiqui, a doctor trained in England, and Ismet, a homemaker. You might think the daughter who eventually got into MIT was the smart one in the family, but her siblings are just as accomplished. Mohammed, Aafia's brother, is an architect living in Houston with his wife, a pediatrician, and their children. Fowzia, Aafia's sister, is a Harvard-trained neurologist who was working at Sinai Hospital in Baltimore until she decided to go back to Pakistan.

Aafia Siddiqui moved to Texas in 1990 to be near her brother and had good enough grades after spending a year at the University of Houston to transfer to MIT. She requested a room in the university's only all-female dorm, McCormick Hall, which consists of two modern, block-like towers set along the Charles. Siddiqui's fellow students say she was a quiet, studious woman who was devout in her religious beliefs but not a fundamentalist. She often wore a headscarf, for example, but didn't cover her face.

"She was religious, but that wasn't unusual in McCormick," says a former MIT student who lived in the dorm at the time. "She was just nice and soft- spoken," says Marnie Biando, a student who worked at the front desk. "She wasn't terribly assertive."

While at MIT Siddiqui apparently joined an association for Muslim students. She wrote three guides for members who wanted to teach others about Islam. On the group's website, Siddiqui explained how to run a daw'ah table, an informational booth used at school events to educate people about, and persuade them to convert to, Islam. Some of what Siddiqui wrote -- about needing enough money to buy Islamic literature and posterboard -- sounds like a handout for a PTA meeting.

Other references, however, reveal a passion for Islam that could be called hard line. In the guides she wrote, "Imagine our humble, but sincere daw'ah effort turning into a major daw'ah movement in this country! Just imagine it! And us, reaping the reward of everyone who accepts Islam through this movement, through years to come . . . Think and plan big." So big was her thinking that she envisioned an outcome that might surprise many of her adopted countrymen: "May Allah give this strength and sincerity to us so that our humble effort continue, and expands until America becomes a Muslim land."

Even in her academic pursuits, Siddiqui's sights were trained on her faith. A biology major, in her sophomore year she won a $5,000 grant to study the effects of Islam on women in Pakistan.

A photo of her on graduation day shows an attractive woman smiling beside the Charles River. She wears a simple necklace and dangling earrings. It's easy to understand why students who knew her were so surprised to hear her name on the nightly news. In the perpetually updated photo gallery of terrorist suspects that has made its way into our living rooms since 9/11, her face is among the most angelic.

Sometime after their daughter's graduation, Siddiqui's parents, concerned about her prospects for marriage, went out and found her a husband. Mohammed Amjad Khan seemed like a great catch. The son of a wealthy family and a medical student, he, like Siddiqui, was a well-educated Pakistani trying to make a life for himself in Boston. He also shared Siddiqui's faith but did not seem threatened by her desire for a career.

Siddiqui, after all, wasn't done with school. She entered Brandeis University as a graduate student in cognitive neuroscience. Though media reports in the past year have erroneously given her such technical-sounding titles as microbiologist, geneticist, and neurologist, the truth is that Siddiqui's training didn't lend itself easily to the type of terrorist acts that haunt us in our worst nightmares.

"They started with the whole idea that Aafia was involved in biochemical warfare," says Sharp. "She wasn't taking brain cells and testing how they reacted to gases. But there's all this news in the media about the changing face of Al Qaeda and the neurobiology scare, and now we've got this MIT graduate with a Brandeis Ph.D. who's cooking up all these viruses."

What Siddiqui was actually cooking up at Brandeis was more mundane. Her graduate work was based on a simple concept: that people learn by imitation. To study this, she devised a computer program and used adult volunteers, who came to her office and watched various objects move randomly across the screen, then reproduced what they recalled. The point was to see how well they retained the information having seen it on the screen.

Paul DiZio, a professor of cognitive neuroscience at Brandeis who was on Siddiqui's dissertation committee, laughs when asked if such work could be applied to Al Qaeda operations. "I can't see how it can be applied to anything," he says. "It's not very applied work. It didn't have a medical aspect to it. And, as a computer expert, she was competent. But you know, calling her a mastermind or something does not seem -- I never saw any evidence."

What DiZio did see evidence of was Siddiqui's obvious passion for Islam. "She made many references to her faith in scientific conversations," he says. "When presenting a proposal about how some results would come out and whether they would support her theory, she would say, 'Allah willing.'" Though such comments may have seemed strange in an academic setting, DiZio says there was nothing radical about Siddiqui. "She just seemed like a very kind person."

She was also a person whose life was rapidly changing. DiZio recalls asking Siddiqui what she would do after earning her Ph.D. "She said something about how she had commitments to her children and her family, and that this is the way it was," he says. Somehow, Siddiqui's plan for a career outside the home had been lost.

By the time Siddiqui finished her dissertation, she and Khan, who was nearing the end of his residency at Brigham and Women's, had two children. According to Sharp, the couple was beginning to argue over how to raise them.

"Aafia wanted to live in the West," Sharp says the family told her, adding that Khan wanted to return to Pakistan and raise the children as conservative Muslims. When Siddiqui's parents had arranged their daughter's marriage to Khan, they were under the impression that he was progressive. Now they were worried.

Hassan Abbas, a Pakistani visiting scholar at Harvard Law School and the author of the recently published Pakistan's Drift into Extremism: Allah, the Army, and America's War on Terror, remembers the story of the couple's marital troubles differently. Once, when speaking with a colleague of Khan's who worked at Massachusetts General Hospital, Abbas was told Siddiqui was the more fundamentalist of the two. But he never met her. When he moved to Boston in 2001, Abbas tried to set up a network of Pakistani academics and hoped to add Siddiqui to his listserv. "To my surprise," he says, "despite my good contacts and friendships, nobody was willing to say even a single word about her."

What is known about the couple is that they lived with their children on the 20th floor of Roxbury's Back Bay Manor, a popular housing choice for medical residents and foreigners seeking medical treatment because of its proximity to the city's hospitals. The apartment was home base for a nonprofit organization the two started with Fowzia in 1999, called the Institute of Islamic Research and Teaching.

The Mosque for the Praising of Allah in Roxbury is a simple brick building with a double arched doorway out front and a Middle Eastern café next door. In his cluttered second-floor office, Abdullah Faruuq, the mosque's imam, crams his tall body behind his desk and crosses his stocking feet on a chair in front of him.

"What I know of her," he says, "is that she was living here in America, and her organization was for sharing Islamic information with the American people."

Siddiqui ordered Korans and other books to be distributed to prisons and on school campuses. Boxes of them would arrive at Faruuq's mosque, and he'd wait for her to come pick them up. Though she was a small woman, Siddiqui never asked for help carrying the heavy boxes down the steep flight of stairs.

Faruuq was impressed with Siddiqui's devotion but says she wasn't a radical. "'As long as it's not evil, I can do it,'" he says, paraphrasing what Siddiqui herself might have said of her acceptance of the western world. "'I show my hands, show my face. I drive my own car. I have my credit cards.' She had all of that. She was an American girl. Put that down: Aafia Siddiqui was an American girl. And a good sister."

Siddiqui's missionary work stemmed from her belief that it was her duty to bolster the Muslim community around her. "She was always very frustrated here that Muslims were not addressing the needs of their community," says a woman who was a student of Siddiqui's. "She said we needed to be doing more to help our people and that we needed to address the needs of the community." She says Siddiqui wanted her husband to use his medical skills to help the less fortunate.

Talal Eid, imam of the Islamic Center of New England in Quincy, also knew Siddiqui through the charitable work she did. He recalls her raising money for Bosnian orphans. "You know, we were all active, but to see a woman who was active in this way was really something nice."

People who lived on the same floor of Back Bay Manor as Siddiqui have a different impression of her. "In some ways we knew her kids better than we knew her," says Matthew Parfitt, who lived down the hall. "She'd leave them to play in the hallway a lot. "

The only people Parfitt noticed going in and out of Siddiqui's apartment were a woman she seemed close to, possibly her sister Fowzia, and an older woman who came to visit for some time, possibly her mother, Ismet.

Another neighbor, Pat Shechter, remembers seeing Siddiqui in the elevator with her son, who was on his way to school. "I said, 'Oh, what do you study in school?' And he said, 'the Koran.'"

The FBI suspects Siddiqui was doing a lot more at Back Bay Manor than sending her kids out to play in the hallway or having her sister over for tea. In the weeks after 9/11, when the FBI was scrambling to make up for past oversights, the agency became suspicious of several people in the building, particularly Khan and Siddiqui. At least some of that suspicion stemmed from the couple's connection to two Saudi nationals with financial dealings that in a post-9/11 world set off warning bells. Workers at Fleet reviewing past bank transactions reportedly flagged as suspicious some that occurred just months before the attacks.

In July 2001, two Saudi nationals, Abdullah Al Reshood and Hatem Al Dhahri, had taken over Khan and Siddiqui's lease when the couple decided to move to Malden (though the Saudi embassy and Sharp deny they lived in the apartment). During that time, Al Reshood received a $20,000 wire transfer from the Saudi government. The money, a Saudi official later explained to the Boston Globe, was sent by the Saudi government to Al Reshood to pay for medical treatment for his wife.

The Fleet employees filed a suspicious activity report, or SAR, with the Treasury Department, which alerted the FBI. Investigators were reportedly stunned when they realized the SAR had been filed for someone so closely connected to Siddiqui and Khan, already under suspicion for having used a debit card to buy night-vision goggles, body armor, and military manuals from American websites, and for donating to charities the FBI watches closely.

When questioned, Sharp says, Khan told authorities he had purchased the military items for big-game hunting in Pakistan, saying goggles and armor weren't available there. Siddiqui, who was questioned only incidentally, was quickly released. Shortly after that, citing the difficulty of living as Muslims in the United States after 9/11, the couple returned to Pakistan.

Siddiqui and Khan stayed in Pakistan for a short time, then returned to the United States. They remained until 2002, then moved back to Pakistan. The tension between the couple had continued to grow and finally reached the breaking point in August 2002. Siddiqui was eight months pregnant with their third child, and she and Khan were now estranged. She and the children stayed at her mother's house, while Khan lived elsewhere in Karachi.

One day, according to Sharp, Khan came over to Aafia's parents' house bearing a letter explaining that he was going to divorce Siddiqui. He started reading the letter, and a heated argument began between Khan and Siddiqui's parents. The fight was too much for Siddiqui's father, Sharp says. He had a heart attack and died. Within weeks, Siddiqui gave birth to a son.

Siddiqui stayed at her mother's house for the rest of the year, returning to the United States without her children around December 2002 to look for a job in the Baltimore area, where her sister had begun working at Sinai Hospital. Siddiqui had interviews at Johns Hopkins and SUNY, says Sharp. The real purpose of her trip, the FBI suspects, was to open a post office box for Majid Khan, a purported Al Qaeda operative who allegedly had plans to blow up gas stations and fuel tanks in the Baltimore-Washington area. Siddiqui's family contends that her trip to Baltimore was for the sole purpose of finding a job, and that if she did open a post office box it was for the replies she hoped to get.

Months later, the FBI would make its most devastating claim against Siddiqui.

It was still dark on the morning of March 1, 2003, when Pakistani authorities arrested Khalid Sheikh Mohammed, a known September 11 mastermind, at a Karachi safe house. The arrest made news around the world. It also presaged the extraordinary vanishing act of Aafia Siddiqui and her three small children.

"Apparently Khalid Sheikh Mohammed gave up Aafia's name as being a major Al Qaeda operative," says Sharp. Asked how he could possibly have known her name if she were innocent of the FBI's claims against her, Sharp says Siddiqui's identity was likely stolen. "Aafia was, I think, probably a pretty naive and trusting person," Sharp says, "and my guess is it would be pretty easy for somebody who wanted to steal an identity to just steal it."

Because of the secretive nature of the interrogation, we may never know what, if anything, Khalid Sheikh Mohammed said about Siddiqui. About a month after his capture in the spring of 2003, however, she disappeared. The last her mother remembers, Siddiqui was piling herself and her kids, then seven, five, and six months old, into a taxi headed to the train station, the first step of what she said was her planned trip to visit an uncle in Islamabad. Her mother said goodbye to her daughter and grandchildren -- and hasn't seen them since.

What happened to Aafia Siddiqui and her children that day is anyone's guess. Siddiqui's mother, Ismet, claims that a few days after Siddiqui's disappearance, a man on a motorcycle arrived at her house in a leather suit and helmet and told her Aafia was being held and that she should keep quiet if she ever wanted to see her daughter and grandchildren again.

A report in the Pakistani Urdu press said that Siddiqui and her kids had been seen being picked up by Pakistani authorities and taken into custody. Even a spokesman for Pakistan's interior ministry and two unnamed U.S. officials confirmed this in the press. Several days later, however, Pakistani and American officials mysteriously backtracked, saying it was unlikely that Siddiqui was in custody.

Ismet, hysterical, decided to board a plane to the United States in an attempt to find her daughter. When official-looking men greeted her at JFK Airport in New York, she thought they were there to help her find her daughter.

"She's detained for four hours by the FBI, NYPD, Homeland Security," says Sharp. "She thinks they're all there to help her. That's how naive she was. And she's crying and saying, 'Tell me where my daughter is,' and they don't know where her daughter is and they let her go."

Siddiqui's sister Fowzia picked up Ismet and took her back to Baltimore. "And the next thing they know," Sharp says, "there's a knock at the door, and it's the FBI and they're very aggressively serving a subpoena for Ismet Siddiqui to come here to Boston to testify before a grand jury." It was then that Siddiqui's brother, Mohammed, who had been referred to Sharp by a professional connection in Houston, hired her to represent the family.

In the days after Ismet Siddiqui was served the subpoena, she, Fowzia, and Mohammed all spoke at length with agents from the FBI and U.S. Attorney's Office. "We just gave them everything," says Sharp. "And they were saying, 'We still think she's got another life that you don't know about.'"

Aafia Siddiqui had been missing for more than a year when the FBI put her photographs on its website. It was May 26, and Ashcroft and Mueller told the press that Siddiqui was an Al Qaeda facilitator -- someone knowledgeable about the United States and fluent in English who can get things done for other operatives.

One month after the FBI press conference, a bombshell from the Wall Street Journal hit Sharp's desk, and she knew it was just the thing she needed. The newspaper broke the story linking the woman involved in the 2001 diamond trade in Liberia (a story detailed by Douglas Farah, a senior fellow at the National Strategy Information Center, in his book Blood from Stones: The Secret Financial Network of Terror) to Aafia Siddiqui.

Sharp says the allegation was a blessing in disguise because it places Siddiqui somewhere at a specific time. She says she can prove Siddiqui was in Boston that week. "If we can show that Aafia was here and not in Liberia, then that's the stone that slays Goliath," Sharp says.

"The rumor among well-informed Pakistanis is that Pakistani intelligence arrested Aafia and then killed her," says Harvard's Hassan Abbas. If Siddiqui was captured, why would she be killed? Generally, terrorism suspects are captured and paraded before the press to show that the government is doing its job. The fact that Siddiqui has been missing so long does not bode well for her reappearance.

"ISI does not keep people for so long," says Muzamal Suherwardy, referring to the Pakistani intelligence agency. The case is unusual, says Suherwardy, a Pakistani journalist, because "it was alleged that she was in the custody of ISI and then she disappeared." If there had been evidence against her, "she could be put under trial in Pakistan."

It's possible Siddiqui was killed while in the custody of ISI. Suherwardy points out that this is especially likely if "she is believed to be a double agent working both for Al Qaeda and ISI." He also wonders if "some high official of ISI" was involved in the Liberian diamond deal.

And the children? "One thing is clear so far," Suherwardy says. "Where she is, her children are there with her."

In her writings about setting up and running a daw'ah table, Siddiqui advised, "As with starting any endeavor, the most important thing is the intention behind it." She then quoted the Muslim prophet Muhammad as saying: "Indeed actions are based on intentions. For every person is what he intended."

Perhaps Aafia Siddiqui intended her life to be one of devotion to her family, education, and religion. Or perhaps she sought a more radical outlet for religious beliefs. Whatever the truth, it's doubtful Aafia Siddiqui ever intended to go missing at the age of 31 -- or to jeopardize the lives of her children, who went missing with her. Whatever her ultimate intention, forces larger than Aafia Siddiqui herself may well have made sure that she will never be seen or heard from again.

As one source who knew Siddiqui in Boston says, "Only God knows where she is now."