Married to al Qaeda: The American educated neuroscientist who wed into 9/11 family and ended up in Kabul shoot-out

Mother-of-three Aafia Siddiqui, 36, an ex-student at the elite Massachusetts Institute of Technology (MIT), was flown to the US on Monday after being held by the military in Afghanistan. 

She is said to have been shot and wounded after trying to kill the agents.

Aafia Siddiqui, in detention in Aghanistan last month, where she was shot during an interrogation

The Americans say they  took custody of Ms Siddiqui last month.

But her family and rights groups say she has spent the last five years in jails secretly run by the US.

US authorities say Ms Siddiqui was married to Ali Abd al-Aziz Ali, a nephew of the man accused of masterminding the 9/11 attacks, Khalid Sheikh Mohammed and a cousin of Ramzi Yousef, who was convicted of the 1993 bombing of the World Trade Centre in New York.

They also claim the U.S.-trained neuroscientist, has links to at least two of 14 suspected high-level al Qaeda members held at Guantanamo Bay.

The story of her arrest, with conflicting versions, is one of the strangest to emerge since the September 11, 2001, al Qaeda attacks on the United States.

The  U.S. Department of Justice said Afghan police arrested Siddiqui after becoming suspicious of her behaviour outside the provincial governor's compound in the city of Ghazni on July 17.

In the family: Siddiqui was married a nephew 9/11 mastermind Khalid Sheikh Mohammed (left) and a cousin of Ramzi Yousef, who was convicted of bombing the  World Trade Centre in 1993

Police found documents describing bomb-making and excerpts from the book, Anarchist's Arsenal, as well as papers describing U.S. landmarks and substances sealed in bottles and jars.

The next day, U.S. soldiers and two FBI agents arrived at the Afghan police station where Siddiqui was being held.

"The personnel entered a second floor meeting room, unaware that Siddiqui was being held there, unsecured, behind a curtain," the department said.

"A U.S. warrant officer placed his rifle on the ground, next to the curtain.

"Shortly after the meeting began, the captain heard a woman yell from the curtain and, when he turned, saw Siddiqui holding the warrant officer's rifle and pointing it directly at the captain.

"The interpreter seated closest to Siddiqui lunged at her and pushed the rifle away as Siddiqui pulled the trigger. Siddiqui fired at least two shots but no one was hit.

The warrant officer returned fire with a 9 mm service pistol and fired approximately two rounds at Siddiqui's torso, hitting her at least once."

Despite being shot, Siddiqui continued to struggle and struck and kicked the officer while shouting in English that she wanted to kill all Americans and then passed out, the statement said.

Afghan police in Ghazni however, told a different story.

Accused: Siddiqui in an undated FBI handout photo

They said officers searched Siddiqui after reports of her suspicious behaviour and found maps of Ghazni, including one of the governor's house, and arrested her along with a teenage boy.

U.S. troops requested the woman be handed over to them, but the police refused, a senior Ghazni police officer said.

U.S. soldiers then proceeded to disarm the Afghan police at which point Siddiqui approached the Americans complaining of mistreatment by the police.

The U.S. troops, the officer said, "thinking that she had explosives and would attack them as a suicide bomber, shot her and and took her".

The boy remained in police custody.

Siddiqui and her three children disappeared from her parents' home in the Pakistani port city of Karachi in 2003 and Pakistani human rights groups said they believed the woman had been held at Bagram, the main U.S. base in Afghanistan.

U.S. officials believe Siddiqui was in Pakistan until her arrest in neighbouring Afghanistan, the New York Times said.

Family members said Siddiqui was raped and tortured at Bagram, although they did not say how they knew this.

"Her rape and torture is a crime beyond anything she was ever accused of," Fauzia Siddiqui told reporters in Karachi.

"For a long time, my family and I have kept our silence because we knew she was innocent and also based on threats of severe consequences if we spoke," she said.

Fauzia Siddiqui said her sister would not receive a fair trial.

If convicted, she faces a maximum sentence of 20 years in prison on each charge.

Ms Siddiqui's lawyer, Elaine Whitfield Sharp, called the charges "a tall story" and disputed claims by the US that her client had been in hiding for several years before her alleged capture in July.