An American-educated neuroscientist who is the only woman accused of working for al-Qaeda’s top leadership appeared in court in New York last night after her capture in Afghanistan.

The US Government alleges that Aafia Siddiqui, a Pakistani mother of three with a biology degree from Massachusetts Institute of Technology and a doctorate in behavioural neuroscience from Brandeis University, near Boston, is married to the nephew of Khalid Sheikh Mohammed, the man who claims to have organised the September 11 terror attacks in 2001.

She is charged with attempted murder and assault for allegedly trying to kill an American interrogator in a gun battle after she was arrested outside an Afghan government compound with a handbag full of chemicals and information on chemical, biological and radiological weapons, as well as descriptions of “various landmarks” in the United States.

Her trial should shed light on the mystery surrounding her disappearance with her children from the Pakistani city of Karachi in 2003. Her family claimed that she was abducted and imprisoned in a secret US detention centre. Six human rights groups, including Amnesty International, have listed her as a possible “secret detainee”.

“What a mockery that after five years in detention Aafia is suddenly discovered in Afghanistan,” her younger sister, Fauzia Siddiqui, a doctor, told a news conference in Karachi yesterday. “Aafia was tortured for five years until one day US authorities announce that they have found her in Afghanistan, which shows how they abused their power and tortured an innocent woman without committing any crime.”

US officials insisted that they had no knowledge of her whereabouts until she was arrested by Afghan police for acting suspiciously outside the governor’s compound in the central Afghan province of Ghazni on July 17. They said that Ms Siddiqui was with a teenage boy at the time.

Prosecutors said that numerous documents were found in her handbag about “the creation of explosives, chemical weapons and other weapons”. Ms Siddiqui is also alleged to have had descriptions of landmarks in the US, documents about US military assets and excerpts from The Anarchist Arsenal.

Two FBI agents escorted by US soldiers interrogated her the following day. The soldiers were unaware that she was being held behind a curtain and a warrant officer put his M4 rifle on the ground.

Ms Siddiqui allegedly grabbed the rifle and fired two shots at a US army captain but an interpreter pushed the gun away as she fired. As the soldiers returned fire, she was hit at least once. “The warrant officer saw and heard Siddiqui fire at least two shots as Interpreter 1 tried to wrestle the gun from her. No one was hit,” the criminal complaint says. “The warrant officer heard Siddiqui exclaim, ‘Allah akbar!’ Another interpreter heard Siddiqui yell in English, ‘Get the f*** out of here!’ as she fired the rifle.”

A slight woman, Ms Siddiqui walked gingerly into court last night with her head wrapped in a scarf. “She is shot. She is in pain. We were able to look at the dressing. You can see it’s stained and oozing,” said Elizabeth Fink, her court-appointed lawyer.

Ms Siddiqui, 36, shook her head as the judge read the allegations about her trying to shoot a soldier. Her lawyer asked for the case to be dismissed.

“I think its ridiculous,” Ms Fink said. “You tell me you can put down an M4 rifle right by your foot and this 90lb \ woman is behind the curtain and you do not realise until the rifle is in her hand,” she said.

The US Government named Ms Siddiqui in 2004 as one of seven suspected al-Qaeda associates feared to be planning an attack. Washington said, however, that it had no information linking her to any specific terror attack and that she had not been charged with any terrorist offences.

Ms Siddiqui is one of three children of Mohammed Siddiqui, a British-trained Pakistani doctor. She moved to the US from Pakistan in 1990 to live with her brother, an architect, and study. While at university she raised money for charitable Islamic causes such as widows and orphans in Bosnia.

After completing her doctoral thesis she married a Pakistani anaesthesiologist and lived in a flat in Boston that also served as the headquarters of an Islamic charity called the Institute of Islamic Research and Teaching. In 2002 the couple were questioned by the FBI after Ms Siddiqui’s husband allegedly purchased night-vision goggles and body armour on the internet. Within months the couple moved back to Pakistan but soon separated.

The US alleged that Ms Siddiqui has links to at least two of the 14 high-level al-Qaeda suspects who were moved to Guantanamo in September 2006. American prosecutors said that Ms Siddiqui opened a post office box in Maryland for Majid Khan, a former Baltimore resident now being held at the US detention centre in Guantanamo Bay.

Ms Siddiqui later married Ali Abd al-Aziz Ali, known as Ammar alBaluchi, a nephew of Khalid Sheikh Mohammed and a cousin of Ramzi Yousef, who was convicted of the 1993 bombing of the World Trade Centre in New York.

Ms Siddiqui faces up to 20 years in prison on each count if convicted. The judge set a bail hearing for Monday.

First-rate minds

— The Massachusetts Institute of Technology (MIT) is a private, university in Cambridge, Massachusetts. It admitted its first students in 1865

— 72 Nobel prize laureates have worked at MIT

— Ranked tenth-best university in the world in 2007 by The Times Higher Education Supplement/ Quacquarelli Symonds survey

— Admission criteria are strict. Last year 12.5 per cent of applicants were offered a place. Total first-year enrolment was 1,069

— 9.2 per cent of students came from outside the United States

— Famous MIT alumni are David Miliband (a postgraduate degree in political science, 1990); Kofi Annan, the former UN Secretary-General; Ahmed Chalabi, the former Iraqi Deputy Prime Minister; and Binyamin Netanyahu, the former Prime Minister of Israel

Sources: MIT; THES/QS survey

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