An American-educated female neuroscientist has been extradited from Pakistan to the United States and is due in court in New York today to face terrorism charges.

The case of Aafia Siddiqui, 36, has caused an outcry in Pakistan amid sharply differing accounts of events.

US prosecutors say that Ms Siddiqui is a suspected al-Qaeda terrorist — near the top of the FBI's most wanted list of fugitive terror suspects — who was detained in Afghanistan three weeks ago, carrying documents about how to make explosives and details of various US landmarks.

They add that she attacked US military officials who arrived at her detention centre to take her away, rushing out from behind curtains, snatching up an assault rifle that had been left lying on the floor, and firing twice before she was shot in the chest and subdued.

Michael Garcia, the US attorney for the southern district of New York, says that Ms Siddiqui has been charged with one count of attempting to kill US officials and one count of assault, each of which carries a maximum penalty of 20 years. The charges have been filed at Manhattan federal court.

But her family say that far from being arrested last month, Ms Siddiqui disappeared from the Pakistani city of Karachi in 2003, along with her three children.

They fear that Ms Siddiqui has been the subject of extraordinary rendition, snatched off the street and held in secret for five years, during which, they suspect, she has been brutally interrogated. Several high-profile al-Qaeda suspects have been held at a detention facility at Bagram airbase in Afghanistan under conditions of such secrecy that they are nicknamed "ghost" prisoners.

One British journalist, Yvonne Ridley, suggested last year that Ms Siddiqui could be the supposed "grey lady of Bagram", a Pakistani woman who has allegedly been held there for years.

"What a mockery that after five years' detention Aafia is suddenly discovered in Afghanistan," said Dr Fauzia Siddiqui, the missing woman's younger sister, at a press conference in Karachi.

She said that the family had received death threats by telephone and text, warning them not to speak about Ms Siddiqui's case. She said that she did not know who was sending the threats.

Ms Siddiqui lived in the US for several years with her first husband, Dr Amjad Khan, studying biology at the elite Massachusetts Institute of Technology (MIT) in Boston. US security officials are said to believe that she was a sleeper agent, whose scientific education allowed her to become one of the few women to gain access to the inner circles of al-Qaeda, with its biological and chemical weapons programme.

She was placed on FBI surveillance inn 2002 after she ordered a flak jacket and book on explosives. She apparently returned to Pakistan in 2002 with her husband and three children and has not been heard of since March 2003, when she took a cab from Karachi to Islamabad to visit her mother

Elaine Whitfield Sharp, Ms Siddiqui’s family lawyer, called the charges " a tall story". She disputed the US Government's earlier claims that Ms Siddiqui had gone underground for several years before her capture.

"I believe she's become a terrible embarrassment to them, but she's not a terrorist," Ms Sharp said. "When the truth comes out, people will see she did nothing wrong."

She said that Ms Siddiqui was not a terrorist, but an innocent woman who had been held at Bagram air base in Afghanistan or elsewhere for the last several years and tortured by some combination of US, Pakistani and Afghan officials.

The Pakistan Government has so far declined to comment on Ms Siddiqui's case, although security officials deny that they arrested Ms Siddiqui in 2003. Pakistan's Inter Services Intelligence has been accused of being party to the scientist's detention.

The former military government of General Pervez Musharraf is suspected of handing her over to the Americans.

Her cause has been taken up by the Human Rights Commission of Pakistan, whose secretary-general, Iqbal Haider, said that the case against her was "false and fabricated". He called for her to be tried by an independent tribunal.

"We demand that Aafia's trial should not take place in Guantanamo Bay. We demand that Aafia's relatives be allowed immediate access to her," Mr Haider told the Karachi press conference.

Her family appealed for her release. "Her absence has given us great pain for the last five years and we have been looking for her and her children," said Dr Siddiqui. "My sister is innocent, she has done no wrong."

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