Robert Fisk: The mysterious case of the Grey Lady of Bagram

How does a neuroscientist and mother of three end up in jail as an al-Qa'ida agent?

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Dr Shams Hassan Faruqi sits amid his rocks and geological records, shakes his bearded head and stares at me. "I strongly doubt if the children are alive," he says. "Probably, they have expired." He says this in a strange way, mournful but resigned, yet somehow he seems oddly unmoved. As a witness, supposedly, to the mysterious 2008 re-appearance of Aafia Siddiqui – the "most wanted woman in the world", according to former US attorney general John Ashcroft – I guess this 73-year-old Pakistani geologist is used to the limelight. But the children, I ask him again. What happened to the children?

Dr Faruqi is Aafia Siddiqui's uncle and he produces a photograph of his niece at the age of 13, picnicking in the Margalla hills above Islamabad, a smiling girl in a yellow shalwar khameez, half-leaning against a tree. She does not look like the stuff of which al-Qa'ida operatives are made. Yet she is now a semi-icon in Pakistan, a country which may well have been involved in her original kidnapping and which now oh-so-desperately wants her back from an American prison. Her children, weirdly, disconcertingly, have been forgotten.

Aafia Siddiqui's story is now as famous in Pakistan as it is notorious in a New York City courtroom where her trial for trying to kill an American soldier in the Afghan city of Ghazni in 2008 – she was convicted this month and faces a minimum of 20 years in prison on just one of the charges against her – is regarded as a symbol of American injustice. "Shame on America," posters scream in all of Pakistan's major cities. She is known as the "grey lady of Bagram", supposedly tortured for five years in America's cruel Afghan prison. Pakistan's President Asif Ali Zardari has asked American envoy Richard Holbrooke to repatriate Siddiqui under the Pakistan-US prisoner exchange scheme, while the Prime Minister Yousuf Raza Gilani has dubbed her a "daughter of the nation". Opposition leader Nawaz Sharif promises to demand her release. But none of them mention the children. Ahmed, Sulieman and Maryam are their names.

Ahmed was returned to Pakistan from Afghanistan in 2008, but Dr Faruqi tells me he doesn't believe for a moment that it is Aafia Siddiqui's son. "He came here to stay with me, but he said he didn't know Aafia until he was taken to Ghazni. He said to me: 'I was in the big earthquake in Afghanistan and my brothers and sisters were killed in their home while I was out fetching water – that's what saved my life.' He told me that after the earthquake, he was put in an orphanage in Kabul. He was shown a photograph of my niece Aafia and said he did not know this lady, that he had never seen her before. Then he was taken to Ghazni and told to sit next to this woman – my niece. The boy is intelligent. He is simple. He is honest."

All such mysteries require a "story-so-far". It goes like this. Aafia Siddiqui, a 38-year-old neuroscientist, an MIT alumna and Brandeis university PhD, disappeared after leaving her sister's home for Karachi airport in 2003, taking Ahmed, Sulieman and Maryam with her. The Americans say she was a leading al-Qa'ida operative. So does her ex-husband. She had re-married Ammar al-Baluchi, currently in Guantanamo Bay, a cousin of Ramzi Yousef who was convicted for the 1993 World Trade Centre bombing. Not, you might, say, a healthy curriculum vitae in the West's obsessive "war on terror". In 2004, the UN identified her as an al-Qa'ida operative.

But released inmates from the notorious American prison at Bagram near Kabul– where torture is commonplace and at least three prisoners have been murdered – have stated that there was a woman held there, a woman whose nightly screams prompted them to go on hunger strike. She was dubbed the "grey lady of Bagram". At her New York trial, Siddiqui demanded that Jewish members of the jury be dismissed, she fired her own defence lawyers who said she had become unbalanced after torture; Siddiqui blurted out that she had been tortured in secret prisons before her arrest. "If you were in a secret prison ... where children were murdered..." she said.

And so to the town of Ghazni, south of Kabul. It was here that Afghan police stopped her in 2008, carrying a handbag which supposedly contained details of chemical weapons and radiological agents, notes on mass casualty attacks on US targets and maps of Ghazni. American soldiers and FBI agents were summoned to question her and arrived in Ghazni without realising that Siddiqui was in the same room, sitting behind a curtain. According to their evidence, she managed to take one of their M-4 assault rifles and opened fire with the words, "Get the fuck of here. May the blood of [unintelligible] be on your [head or hands]." She missed but was cut down by two bullets from a 9mm pistol fired by one of the soldiers. Hence the charges. Hence the conviction.

She wasn't helped by an alleged statement by Khalid Sheikh Mohammed – the man who supposedly planned 9/11 and who is the uncle of her second husband, Ammar al-Baluchi – who claimed that Aafia Siddiqui was a senior al-Qa'ida agent. But then, he'd just been waterboarded 183 times in a month – which hardly makes his evidence, to use a phrase, water-tight.

The questions are obvious. What on earth was a Pakistani American with a Brandeis degree doing in Ghazni with a handbag containing American targets? And why, if her family was so fearful for her, didn't they report her missing in 2003, go to the press and tell the story of the children? Ahmed – son of Siddiqui or Afghan orphan, depending on your point of view – is now staying with Siddiqui's sister, Fauzia, in Karachi; but she refuses to let him talk to journalists. The Americans have shown no interest in him – even less in the other two, younger children. Why not?

It's odd, to say the least, that Dr Faruqi also maintains that in 2008 – before the Ghazni incident – Aafia Siddiqui turned up at his home in the suburbs of Islamabad. "She was wearing a burqa and got out of the car, just outside here," he says, pointing to the tree-lined street outside his office window. "I only caught sight of her once, and I said 'You have changed your nose'. But it was her. We talked about the past, her memories, it was her voice. She said the ISI (the Pakistani Inter-Services Intelligence) had let her come here. She wanted to get away, to go back to Afghanistan where she said the Taliban would protect her. She said that since her arrest, she knew nothing of her children. Someone told her they had been sent to Australia."

More questions. If Siddiqui was a "ghost prisoner" in Afghanistan, how come she turned up at Dr Faruqi's home in Islamabad? Why would she wear an Afghan "burqa" in the cosmopolitan capital of her own country? Why did she not talk more about her children? Why could she not show her face to her own uncle? Did she really come to Islamabad?

Fauzia Siddiqui is now touring Pakistan to publicise her sister's "unfair" trial, her torture at the hands of Americans. Most of the Pakistan press have taken up her story with little critical attention to the allegations against her. She has become a proto-martyr, a martyr-in-being; if her story is comprehensible, it requires a willing suspension of disbelief. But America's constant protestations of ignorance about her whereabouts before 2008 have an unhappy ring about them.

And the children? Rarely written about in Pakistan, they, too, in a sense, were "disappeared" from the story – until the Afghan President, Hamid Karzai, paid an uneasy visit to Pakistan this week and, according to Fauzia, told the Interior minister, Rehman Malik, that "the children of Aafia Siddiqui will be sent home soon". Was Karzai referring to the other two children? Or to all three, including the "real" Ahmed? And if Aafia's two/three children are in Afghanistan, where have they been kept? In an orphanage? In a prison? And who kept them? The Afghans? The Americans?

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