There are a lot of sources for information about Aafia Siddiqui. Principal among them, let me mention the timeline here, and the newly updated DrAafia.org. For court documents there is an out of date listing here, and more recent listing at NEFA, here. This piece in Boston Magazine is definitive for her early (with respect to the U.S.) biography.

So her biography. She was born in Karachi Pakistan in 1972, and according to the FBI wanted material issued in 2003, lived in Zambia, returning to Pakistan to start primary school. Her father was a neurologist (British trained), her mother, a "homemaker" but also an activist for spreading Islam, and possibly an active member of Jamait-e-Islamiya, a conservative Islamic political party in Pakistan. Her brother is an architect in the Houston area, her sister a neurologist in Karachi. She moved to Houston to live with her brother in 1990 and attended University of Houston for a year before transfering to MIT, class of ’95, where she majored in biology, and wrote one paper of note, a Carroll L. Wilson Award paper called, "Islamization in Pakistan and its Effects on Women." She lived in a women’s dorm, and joined the campus Muslim association, and maintained a table where she gave out literature on Islam.

She went to Brandeis for graduate school, getting her Ph.D. in Cognitive Neuroscience (Psychology department) under Robert Sekuler, dissertation title, Learning Through Imitation. It’s listed at UMI, I haven’t read more than the abstract, she did experiments on tracking and learning on computer screens, so it was visual memory stuff. During her time at Brandeis, she married Mohammed Amjad Khan, who was doing a residency at Brigham and Women’s Hospital as an anesthesiologist. During this time, they lived in Roxbury, she did numerous fund raisers for various causes, may or may not have contributed to organizations that were banned or were later banned, and, importantly to my mind, contributed to helping Bosnian orphans.

There is a bunch of stuff about her and her husband after September 11th, they were interviewed by the FBI in 2001. The subjects were her husband’s purchase of night vision goggles, he said for a safari in Pakistan, the FBI thought maybe to aid terrorists, neither was arrested, and they were also questioned on the fact that the people who rented their apartment when they gave it up got funding from the Saudi royal family, and bought out their deposit with it.

Also during that time, they had two children, Ahmed and Maryam, and there were allegations or suspicions of domestic abuse, and one domestic dispute that had something to do with throwing a baby bottle at Aafia cutting her lip.

If all that stuff seems trivial, it isn’t, it turns out, but that’s another story.

They went back to Pakistan in 2002, and the third child, Suleman, was born, and Amjad Khan presented divorce papers to Aafia’s parents, ending their marriage. Aafia makes one trip to the U.S. during December/January, her family says to look for a job, the FBI says to open a post office box for Majid Khan to facilitate a plot to blow up gas stations. It should be not that hard a thing to verify, she supposedly had interviews at two places, one of which was Johns Hopkins, but I haven’t verified the job interviews. The post office box key was among Uzair Paracha’s possessions when he was arrested, according to court documents and newspaper articles.

I am clear that these people tried to facilitate Majid Khan’s entry into the United States. The question is why. All parties agree (FBI, CIA, al Qaeda, the Parachas, Majid Khan himself, etc., etc.) that Majid Khan had been living in Baltimore and went to Pakistan in 2002. All parties agree that he left his asylum papers in Baltimore, and that he tried to get a new copy of them sent to him by having Uzair Paracha impersonate him in a phone call to the U.S. Department of State to request them (copies of asylum papers may only be applied for from within the borders of the U.S. was the problem). But the U.S. says this was all part of a plot (see below), and the others say that he was trying to arrange the new papers, and was told to go to a party where there would be people who could help him (the Parachas). That would not be an uncommon story in black market or word of mouth deals in that part of the world. All agree KSM was at the party, nobody agrees on whether or not the deal had anything to do with him, or therefore, with al Qaeda.

Aafia Siddiqui returned to Pakistan in January 2003 without finding a job, and lived with her parents in Karachi. In March, the CIA began interrogating Khalid Shaykh Mohammad. He mentioned her in his plot concerning Majid Khan, Iyman Faris, and Ammar al-Baluchi (KSM’s nephew). The plot was to use Majid Khan’s expertise in the U.S. energy infrastructure, to wit, he had extensive knowledge because he ran the cash register at his father’s gas station, to wreak havoc by blowing up gas stations, crippling the energy infrastructure. Iyman Khan, you may remember, is doing time for plotting to deconstruct the Brooklyn Bridge by climbing up on the suspension cables and attacking them with an oxyacetylene torch. Also part of the plan divulged by KSM was that Aafia Siddiqui had secretly married Ammar al-Baluchi.

The Pakistani and American authorities started rounding up the constituents of these plots immediately, grabbing Majid Khan and Ammar al-Baluchi during March. Both went to black sites until August 2006, and then Guantanamo Bay (where Majid Khan tried to commit suicide three times by chewing through his radial artery at the elbow, and was unfit for trial and whose case was dismissed by Susan Crawford on torture grounds).

On March 29, 2003, Aafia Siddiqui left her parents’ place by taxi with her three children, to take them to her uncle’s place in Islamabad for safe keeping since the FBI had issued a wanted notice for her arrest and it was "all over the TV" in Pakistan. They never arrived. NBC announced that she’d been arrested by the FBI. The Siddiqui family says Pakistani Intelligence took her, her Ismet mother said she was told by someone who came to the house on a motorcycle but didn’t remove his helmet that she should be quiet about it if she wanted to see her daughter or grandchildren again. Her family retained Elaine Sharpe in the U.S., and her mother traveled once to the U.S. to seek information about her, and got interrogated by the authorities when she did. The FBI subsequently denied that she was in their "custody" or that they knew her "whereabouts".

Aafia Siddiqui says she was injected with a drug and woke up in a cell, she is not sure where. She says she was interrogated by multiple people, and thinks one of them was one of her former classmates from MIT, both because of his familiarity with her work and his Indian accent (meaning that his Urdu or English sounded like he came from India). Binyam Mohammed and Moazzam Begg are pretty sure they saw her at Bagram, and Lord Nazir says he obtained documents that she was at Bagram, although he may mean that Prisoner 650 was a woman and was at Bagram, it isn’t clear.

Charges, meanwhile, continued to mount, with the FBI issuing a "terrorist most wanted" poster in 2004 with her on it among others. The prosecutor at the ICT-Sierra Leone trial alleged she was an operative who facilitated $30 million in blood diamonds in 2001 for al Qaeda, claiming to recognize her from the wanted poster. It’s highly unlikely, since she was just finished with her dissertation, was putting together a journal article, was supposedly baby sitting the neighbors kids together with her own in Roxbury at the time. Even other investigators feel that one is misplaced identity, since she would have needed to go to Pakistan, cross into Afghanistan, come out of Afghanistan, fly to Africa, do the deal for a week, then fly back to Quetta and become untraceable again in Afghanistan, and then make it back to the U.S. without being noticed, all in time for September 11th and her later inquiry with the FBI over her husband’s goggles.

She also morphed into an expert microbiologist working on biological weapons, who did her learning at MIT just the next building over from the anthrax lab and so forth (her biology degree was undergraduate, and it was a combination of biology and anthropology). She became a high ranking "fixer" for al Qaeda, and morphed into al Qaeda’s Mata Hari around this time.

She entered multiple missing persons lists, Asian Human Rights Committee, Pakistan Human Rights Commission of Pakistan, Amnesty International. She was one of the names that became a question mark when President Bush said he emptied the black sites in August 2006. Allegations from Binyam Mohamad and Moazzam Begg are that she was subjected to torture, that she was repeatedly raped, and that she "lost her mind" and they could hear her screaming. Binyam Mohamad says he was conditioned to dismiss her because the U.S. military put out a rumor among the prisoners that she was an informer. Note that most of Moazzam Begg’s comments were made about Prisoner 650 before she became identified with that prisoner, both Moazzam Begg and Binyam Mohamad said they recognized her from her picture (the one with her wearing the black shawl and looking unhealthy). She herself says she was tortured by threatening her children, and that she was shown a picture of her son (it isn’t clear which one) lying in a pool of his own blood. She also says she was kept in extreme isolation and tortured.

Blogs started up to keep her memory alive, although according to Elaine Sharpe, during that period, her family thought she was dead.

Around June to early July, 2008, Yvonne Ridley of cageprisoners started writing and speaking about "The Grey Lady of Bagram – Prisoner 650", based largely on Moazzam Begg’s book and subsequent conversations with Mr. Begg. Lord Nazir (Britain) and Ismail Khan, a Pakistani cricket player turned politician, took up the cry, with first Ismail Khan, then Lord Nazir, then others linking Prisoner 650 with Aafia Siddiqui by about July 12th. She was subsequently arrested on July 17th in Ghazni by the side of the road, by the Ghazni police on an anonymous tip, with her son Ahmed. The U.S. military at first denied there had ever been female prisoners at Bagram (under the Geneva Conventions they must be held separately from the men with special considerations), and for even longer denied the existence of child prisoners in Afghanistan. Subsequent to Aafia Siddiqui’s arraignment, when things were heating up over the release of her son Ahmed, Lt.Col. Rumi Nielson-Green, CENTCOM spokeswoman, admitted there had been a female prisoner, that she had been Prisoner 650, but said she was not Aafia Siddiqui and was held from 2003-2005 and repatriated to her country of origin. The State Department has since reported to the U.N. that there have been 2100+ children held prisoner in Afghanistan for an average length of imprisonment of 1 year.

I think I’ll stop there, and see if there is interest in more, and in sourcing (since I wrote most of this from memory with my papers on the desktop).