By Syed Shoaib Hasan
BBC News, Islamabad
Accounts differ as to how Aafia Siddiqui ended up in American custody Afghan officials have handed over to Pakistan the son of a US-trained Pakistani academic with alleged links to al-Qaeda. Twelve-year old Mohammed Ahmed, son of Dr Aafia Siddiqui, has been handed over to the Pakistani embassy in Kabul. Dr Siddiqui, 36, is currently facing trial charged with attempting to kill American soldiers in Afghanistan. But her lawyers and human rights groups say she has spent the last five years in secret US jails. "I can confirm that Ahmed is now in our custody", Naeem Khan, a Pakistani official, told the BBC. It was not immediately clear if the boy - who was named in documentation in Afghanistan as Ali Hassan - would be returned to his family in Pakistan. Afghan officials produced Dr Siddiqui and her son at a press conference in Ghazni province in July. They say the duo were arrested after being seen "loitering suspiciously" near the local US consulate. US officials later said Dr Siddiqui had been injured during questioning. They allege that she grabbed a rifle during an interrogation session and tried to shoot an FBI official, but was shot herself in the exchange. Subsequently, Dr Siddiqui was moved to the New York, where she is currently under trial for the attempted murder and assault of US officials. But international human rights organizations and Dr Siddiqui's family tell a different story. 'Told to stay quiet' They say that Dr Siddiqui, an ex-student at the elite Massachusetts Institute of Technology (MIT), and her three children disappeared after leaving her parent's house in Karachi on 30 March, 2003. Her two elder sons were seven and five-years old at the time, while her daughter was eight-months old. Mohammed Ahmed - his mother's detention In the immediate aftermath of her disappearance, Pakistan and US officials confirmed she was in their custody. But a couple of weeks later, they denied having any knowledge of her whereabouts. Dr Siddiqui's family have repeatedly said that she was being held by the US authorities in the Bagram air base in Afghanistan. They said they had been visited by local and US officials who had told them to stay quiet and that Dr Siddiqui would be returned soon. But it was only after a British journalist, Yvonne Ridley, reported about 'Prisoner 63' in Bagram airbase that international attention focused on the case. Ms Ridley said that she believed Dr Siddiqui was the mysterious 'Prisoner 63', also known as the grey lady of Bagram, allegedly the only female prisoner held at the base. US officials deny that any female prisoner has ever been held at Bagram airbase. But, within a couple of weeks of the report by Ms Ridley and another one by the Asian Human Rights Commission, Dr Siddiqui and her son were found in Ghazni. 'Treasure trove of information' Dr Siddiqui's case has since then attracted a great deal of attention in Pakistan and the United States. In Pakistan, she is seen as the innocent victim of the country's dealings with the US in the 'war on terror'. Her alleged confinement and treatment has greatly contributed to the anti-American feelings in Pakistan. Aafia Siddiqui studied biology at the Massachusetts Institute of Technology In the United States, she is portrayed as an al-Qaeda agent who, in the words of a US official quoted in the New York Times, "has proved to be a treasure trove of information." Dr Siddiqui is said to have been married to a nephew of Khalid Sheikh Mohammad at the time of her disappearance. As her trial continues, calls have been raised in Pakistan to recover her children. Mohammad Ahmed's handover is believed to be the first part of this process. Her five-year old daughter is still believed to be in Afghan custody, while Dr Siddiqui's says her other son has died.
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The 12-year-old son of neuroscientist and MIT graduate , Mohammad Ahmed, was handed over to his aunt  in Islamabad after years of detention in a  in Afghanistan. Dr. Aafia Siddiqui is still currently facing trial charged with attempting to kill American soldiers in Afghanistan. Siddiqui and her three children disappeared after leaving her parent's house in  on 30th March, 2003. She was married to a nephew of , the accused mastermind of the  attacks. Her husband was captured in 2003 and is now held at the Guantanamo Bay Detention Center. In 2004, Dr. Aafia was identified by the FBI as an “Al-Qaeda operative and facilitator who posed a clear and present danger to America". 

Mohammad Ahmed's mother, Aafia Siddiqui.Mohammad Ahmed was only six when he and his mother, brother and sister were abducted from Karachi in 2003 and later handed over to US authorities. Dr. Fauzia told journalists after the boy had been given to her by officials of the interior ministry and intelligence agencies. She gave a written statement to the officials expressing her gratitude to the Pakistani nation, President of Pakistan Asif ali Zardari, Prime Minister Yousaf Raza Gilani, Advisor on Interior Rehman Malik, Interior Secretary Syed Kamal Shah and the National Assembly and Senate for freeing the boy.

Mohammad Ahmed arrived at the  in Islamabad from Kabul in a PIA flight and was taken to his aunt’s residence.  co-chairman Iqbal Haider said that the daughter of Dr. Aafia was also in Afghanistan. He regretted that despite having U.S. nationality, the U.S. government did nothing for the release of its four citizens, stating that “this is a severe violation of the US laws and constitution.”

Muhammad Ahmed landed back to his home in Karachi from where he had disappeared five years back, with his family, Dr. Fauzia and her family hoping that the other two missing children would also be back home soon, by taking some positive steps from the Government of Pakistan.