By Syed Shoaib Hasan
BBC News, Islamabad
Some reports say Aafia Siddiqui was part of an al-Qaeda sleeper cell
Aafia Siddiqui, whom the US accuses of al-Qaeda links, vanished in Karachi with her three children on 30 March 2003.
The next day it was reported in local newspapers that a woman had been taken into custody on terrorism charges.
Initially, confirmation came from a Pakistan interior ministry spokesman.
But a couple of days later, both the Pakistan government and the FBI publicly denied having anything to do with her disappearance.
Two days after Aafia Siddiqui went missing, "a man wearing a motor-bike helmet" arrived at the Siddiqui home in Karachi, her mother told the BBC.
"He did not take off the helmet, but told me that if I ever wanted to see my daughter and grandchildren again, I should keep quiet," Ms Siddiqui's mother told me over the phone in 2003.
The mother also related the affair to other newspapers.
But the government continued to deny having anything to do with her daughter's disappearance.
This is despite the fact that Mrs Siddiqui's other daughter, Fauzia, says she was told by then Interior Minister Syed Faisal Saleh Hayat in 2004 that her sister had been released and would return home shortly.
Research at the time refused to turn up anything on the status of Aafia Siddiqui - she was not listed as wanted by any federal or Pakistani agency.
At that point, it seemed she had vanished off the face of the earth.
Aafia Siddiqui is the youngest of three children of a British-trained doctor.
Her brother is an architect based in Houston, while Fauzia is a neurologist who used to work at Mount Sinai hospital in New York.
Aafia Siddiqui went to school in Karachi and graduated with a biology degree from the Massachusetts Institute of Technology (MIT) in the US.
Demonstrations have been held in Karachi calling for Ms Siddiqui's release
It was during this time that she got actively involved in on-campus Islamic activities.
A fellow Pakistani student recalls her as being one of the "hello, brother" types.
"They were the ones with scarves who used to get after us to come to the association meetings," the student, Hamza, told the BBC.
"I remember Aafia as being sweet, mildly irritating but harmless. You would run into her now and then distributing pamphlets."
After graduation, Aafia Siddiqui married Muhammad Amjad Khan, a young Pakistani doctor in Boston.
She continued with her studies, enrolling in Brandeis University near Boston for a PhD in neuro-cognitive science. Her degree has often been misreported as being in microbiology or genetics.
At that time, her main problems arose from married life. She and her husband argued over where to bring up their children.
"Aafia wanted them to be brought up in the US and receive a Western education, but Amjad was against it," her mother said in 2003.
The 11 September 2001 attacks in the US changed everything. Her husband was detained by the FBI for questioning.
Aafia Siddiqui reappeared five years later in US custody in Afghanistan
The reason was his purchase of night vision goggles, body armour and military manuals.
He is said to have told the FBI it was for big-game hunting.
Aafia Siddiqui was also questioned briefly, but later released, as was her husband.
Soon, they decided to return to Pakistan, citing the increasing discrimination against Muslims in the US following the 9/11 attacks.
In Pakistan, the already estranged couple soon separated, and they divorced in 2002, while she was pregnant with their third child.
Following the birth, Aafia Siddiqui worked briefly in Baltimore, US, before returning to Pakistan in December 2002, where she disappeared months later.
Various theories about her disappearance started to appear in international and local publications.
The first of these was on 23 June 2003 - three months after her disappearance - in Newsweek.
An investigative report, calling her a micro-biologist, said she and her husband were part of an al-Qaeda sleeper cell.
In Baltimore, she is alleged to have opened a mailbox for a suspected al-Qaeda operative now in Guantanamo Bay.
Majid Khan has been accused of planning to blow up petrol stations across the US.
The charges started to mount.
In 2004 then-FBI director Robert Mueller announced at a press conference that Aafia Siddiqui was wanted for questioning.
She was later named as part of an alleged al-Qaeda diamond smuggling operation in Liberia.
Publications such as Newsweek quoted the FBI as saying this was to finance al-Qaeda's biological and chemical weapons programme.
After that, her name remained on the list of disappeared - until she surfaced last month in Afghanistan in US military custody.
Sister speaks out
Aafia Siddiqui is now in the US facing charges of assaulting and attempting to kill US personnel while in detention in Afghanistan.
The FBI has been unable to make any of the other charges stick.
"It is always believed one is innocent until proven guilty, not the other way round," her sister, Fauzia, told reporters in Karachi on Tuesday.
She added that every time she had met US officials, they had said they had never formally accused Aafia Siddiqui of being a terrorist.
Ex-security officials also point out that if Ms Siddiqui was detained for being a terror suspect, her ex-husband, who is free, should have been too.
Why, then, would Aafia Siddiqui have been arrested and kept in secret confinement for so long?
The answer may lie in her relationship with the family of alleged 9/11 mastermind Khalid Sheikh Mohammed.
Aafia Siddiqui is said to have married Ali Abd'al Aziz Ali, one of his nephews following her divorce.
Although her family denies this, the BBC has been able to confirm it from security sources and Khalid Sheikh Mohammed's family.
It is an open secret in Karachi, that any member of Khalid Sheikh Mohammed's family deemed to be "a 1% threat to US security" is in American custody.
That may be the only "crime" that Aafia Siddiqui has committed.
In the eyes of US and Pakistani security officials, it was apparently too big to ignore.