Aafia Siddiqui
Born/Date of Birthday: 2 March 1972
Place of Birth: Karachi, Sindh, Pakistan
Alma mater: Massachusetts Institute of Technology (BS), Brandeis University (PhD)
Height: 5 ft 4 in (1.63 m)
Board member of: Institute of Islamic Research and Teaching (President)

Criminal charge(s): Attempted murder, assault with a deadly weapon
Criminal penalty: Convicted; sentenced to 86 years in prison
Criminal status: Held in the FMC Carswell, Fort Worth, Texas, U.S.

Spouse(s): Amjad Mohammed Khan​(m. 1995; div. 2002)​allegedly Ammar al-Baluchi, also known as Ali Abdul Aziz Ali (February 2003 – present)
Children: Mariam Bint Muhammad, Ahmed Siddiqui, Suleman
Siblings: Fowzia Siddiqui, Mohamed Siddiqui
Parents: Ismet Faroochi, Muhammad Salay Siddiqui

Scientific career
Fields: Neuroscience
Thesis: Separating the components of imitation (2001)
Doctoral advisor: Robert Sekuler

Aafia Siddiqui (born 2 March 1972) is a Pakistani neuroscientist convicted of multiple felonies over an alleged assault on United States personnel while detained at the Afghan National Police facility in Ghazni, Afghanistan. She is currently serving an 86-year sentence at the Federal Medical Center, Carswell in Fort Worth, Texas. Her case has been described as "one of the most troubling in the sordid history" of the War on Terror. She has also been described as having an "iconic status in the Muslim world" by people that "are angry with American imperialism and domination."

Siddiqui was born in Pakistan to a Sunni Muslim family. For a period from 1990, she studied in the United States. She attended MIT with a full scholarship and obtained a Ph.D. in neuroscience from Brandeis University in 2001. She returned to Pakistan for a time following the 9/11 attacks and again in 2003 during the war in Afghanistan. Khalid Sheikh Muhammad named her a courier and financier for Al-Qaeda, and she was placed on the FBI Seeking Information – Terrorism list; she remains the only woman to have been featured on the list. Counter-terrorism groups have dubbed her "Lady al-Qaeda" and U.S. officials once described her as "the most wanted woman in the world". The New York Times and The Nation have mentioned that these accusations were never brought to court.

In March 2003, she traveled with her three children to Islamabad to visit her uncle, according to her parents, but never arrived and was detained by Pakistani security forces. She and her children were "forcibly removed" and they "disappeared without a trace," with the youngest still missing. Six human rights groups, including Amnesty International, believed she had been illegally detained and interrogated by Pakistani forces, possibly at the behest of the U.S., and even listed her as a possible ghost prisoner held by the U.S.

Five years later, four men that escaped captivity from the prison at Bagram Airfield mentioned in a series of interviews about a Pakistani woman (known only as "Prisoner 650") who was routinely tortured at the prison. Later that year, Siddiqui reappeared in Ghazni, Afghanistan, was arrested by Afghan police when, according to US Authorities, allegedly found in possession of sodium cyanide as well as documents regarding "dirty bombs", chemical weapons and New York City landmarks. The next day, while held for questioning by Afghan authorities, she was shot in the abdomen multiple times, with visiting FBI and Army personnel declaring it as return fire and accusing her of allegedly shooting at them with an M4 carbine from the floor, and Siddiqui denying touching the gun to Pakistani Government Officials, saying she stood up to see who was on the other side of the curtain, and that after one of the startled soldiers claimed she was free, she was shot, and upon regaining consciousness, heard "We could lose our jobs."

She was treated and then extradited to the U.S., where in September 2008 she was indicted on charges of assault and attempted murder, charges to which she pled not guilty. She was convicted on 3 February 2010. NBC mentioned that she was convicted "with a terror enhancement", although The New York Times mentioned upon the conviction that it was unrelated to terrorism, and human rights advocate Mauri' Saalakhan described it on an article on WRMEA as "federal enhancements that didn't make sense." She was later sentenced to 86 years in prison, over arguments by her defense citing a lack of forensic evidence and conflicting accounts of the nine testifying witnesses. Another point of contention was whether she was mentally fit to stand trial, and she is now held at a prison for women with special mental health needs. She was not charged with terrorism-related offenses, being convicted on multiple counts of attempted murder and assault.

Her case has been called a "flashpoint of Pakistani-American tensions", and "one of the most mysterious in a secret war dense with mysteries". She is viewed by many in Pakistan as the "national symbol of honor and victimization", and her arrest and conviction occasioned large protests throughout the country. Various Pakistani movements have since advocated for her release, though other Pakistanis have called this "knee-jerk Pakistani nationalism". The Pakistani news media has portrayed her trial as a farce while the U.S. news media has noted she "is a cause célèbre in the terrorist world,", as opposed to British Muslim online newspaper 5Pillars referring to her as a "cause célèbre in the Muslim world." Mainstream American Muslim groups have considered her as an innocent political prisoner and dozens of people have protested in favor of freeing her in the U.S., joined by religious groups and human rights activists worldwide. Former Pakistani Prime Minister Gilani described Siddiqui as a "daughter of the nation", and current Pakistani Prime Minister Imran Khan has expressed support for freeing Siddiqui on multiple occasions. The Pakistani Senate has unanimously passed resolution no. 399, calling for Siddiqui's repatriation to Pakistan.

While mainstream Muslim groups have long advocated for her release or repatriation, militant groups have also demanded her release. ISIS offered to trade abductees for her on two occasions: once for James Foley and once for Kayla Mueller. Peter Bergen of CNN has described her as an "icon for terrorists" and notes she is "used as a rationale for terrorism against Americans" such as in the Colleyville synagogue hostage crisis, an act which was condemned by her family. Siddiqui herself opposes violent actions from being committed in her name.

Background
Siddiqui came to the United States on a student visa in 1990 for undergraduate and graduate education and eventually settled in Massachusetts. While completing the requirements for her master's degree and her Ph.D. in neuroscience in less than four years, she found time to marry and start a family, and volunteer with the Muslim Student Association and Al-Kifah Refugee Center, proselytizing, urging greater religious observance among Muslims, and doing charity work. Immediately following the 9/11 attacks she returned to Pakistan but then returned to America where her husband was completing his board exams. Later, she divorced her husband and in March 2003 disappeared with her three young children, shortly after the arrest in Pakistan of her second husband's uncle, Khalid Sheikh Mohammed, the alleged chief planner of the 11 September 2001 attacks. Khalid Mohammed reportedly mentioned Siddiqui's name while he was being interrogated, and shortly thereafter she was added to the FBI Seeking Information – War on Terrorism list.

Her whereabouts were reported to have been unknown until she was arrested in July 2008 in Afghanistan. Upon her arrest, the Afghan police reported she was carrying in her purse handwritten notes and a computer thumb drive containing recipes for conventional bombs and weapons of mass destruction, instructions on how to make machines to shoot down US drones, descriptions of New York City landmarks with references to a mass casualty attack, and two pounds of sodium cyanide in a glass jar.

Siddiqui was shot and severely wounded at the police compound the following day. Her American interrogators said she grabbed a rifle from behind a curtain and began shooting at them. Siddiqui has denied this and said she simply stood up to see who was on the other side of the curtain and startled the soldiers, one of whom then shot her. She received medical attention for her wounds at Bagram Air Base and was flown to the US to be charged in a New York City federal court with attempted murder and armed assault on US officers and employees. The government had accused her of "faking mental illness", as they denied she had been kidnapped, despite other psychologists saying she was mentally ill and unfit to stand trial. After receiving psychological evaluations and therapy, the judge agreed with the government psychiatrists declared her mentally fit to stand trial. Siddiqui interrupted the trial proceedings with vocal outbursts and was ejected from the courtroom several times. The jury convicted her on all charges in February 2010. The prosecution argued for a life term. Despite government psychiatrists' accusations of her "faking a mental illness," she is now held at a prison for women with special mental health needs.

Amnesty International monitored the trial for fairness. In a letter to Barack Obama, four British Parliamentarians (Lord Ahmed, Lord Sheikh, Lord Patel, and MP Mohammad Sarwar), protested the arrest, calling it a violation of the Sixth Amendment to the United States Constitution. Many of Siddiqui's supporters, including some international human rights organisations, claimed that Siddiqui was not an extremist and that she and her young children were illegally detained, interrogated, and tortured by Pakistani intelligence, U.S. authorities, or both, during her five-year disappearance. The U.S. and Pakistan governments have denied all such claims.

Biography
Family and early life
Siddiqui was born in Karachi, Pakistan, to Muhammad Salay Siddiqui, a British-trained neurosurgeon, and Ismet (née Faroochi), an Islamic teacher, social worker and charity volunteer. She belongs to the Urdu-speaking Muhajir, Deobandi community of Karachi. She was raised in a pious, observant Muslim household, although her parents combined devotional Islam with their resolve to understand and use technological advances in science.

Her mother, Ismet Siddiqui was prominent in political and religious circles, teaching classes on Islam wherever she lived, founding a United Islamic Organization, and serving as a member of Pakistan's parliament. Her support for strict Islam in the face of feminist opposition to the Hudood Ordinances drew the attention of General Muhammad Zia-ul-Haq who appointed her to a Zakat Council. Siddiqui is the youngest of three siblings. Her brother, Muhammad, studied to become an architect in Houston, Texas, while her sister, Fowzia, is a Harvard-trained neurologist who worked at Sinai Hospital in Baltimore and taught at Johns Hopkins University before she returned to Pakistan.

Siddiqui attended school in Zambia until the age of eight and finished her primary and secondary schooling in Karachi.

Undergraduate education
Siddiqui moved to Houston, Texas, on a student visa in 1990, joining her brother who was studying architecture. She attended the University of Houston where friends and family described her interests as limited to religion and schoolwork. She avoided movies, novels and television, except for the news. After three semesters, she transferred to the Massachusetts Institute of Technology.

In 1992, as a sophomore, Siddiqui won a $5000 Carroll L. Wilson Award for her research proposal "Islamization in Pakistan and its Effects on Women". She returned to Pakistan to interview architects of the Islamization and the Hudood Laws, including Taqi Usmani, the spiritual adviser to her family. As a junior, she received a $1,200 City Days fellowship through MIT's program to help clean up Cambridge elementary school playgrounds. While she initially had a triple major in biology, anthropology, and archaeology at MIT, she graduated in 1995 with a BS in biology.

At MIT Siddiqui lived in the all-female McCormick Hall. She continued to be active in charity work and proselytising. Her fellow MIT students described her as being religious, which was not unusual at the time, but not a fundamentalist, one of them saying that she was "just nice and soft-spoken." She joined the Muslim Students' Association, and a fellow Pakistani recalls her recruiting for association meetings and distributing pamphlets. Siddiqui began doing volunteer work for the Al Kifah Refugee Center after returning from Pakistan. Al Kifah included members who assassinated Jewish ultranationalist Meir Kahane and helped Ramzi Yousef with the 1993 World Trade Center bombing. She was known for her effectiveness in shaming audiences into contributing to jihad and the only woman known to have regularly raised money for Al-Kifah. Through the student association she met several committed Islamists, including Suheil Laher, its imam, who had publicly advocated Islamization and jihad before 9/11.

Siddiqui's commitment to al-Kifah showed no sign of dimming when the connection between its Jersey City branch and the World Trade Center bombing became apparent. When the Pakistani government helped the US arrest and extradite Ramzi Yousef for his role in the bombing (where Yousef hoped to kill 250,000 Americans by knocking one WTC tower over into the other) an outraged Siddiqui circulated the announcement with a scornful note deriding Pakistan for "officially" joining "the typical gang of our contemporary Muslim governments", closing her email with a quote from the Quran warning Muslims not to take Jews and Christians as friends. She wrote three guides for teaching Islam, expressing the hope in one: "that our humble effort continues ... and more and more people come to the [religion] of Allah until America becomes a Muslim land." She also took a 12-hour pistol training course at the Braintree Rifle and Pistol Club, mailed US military manuals to Pakistan and moved from her apartment after the FBI agents visited the university looking for her.

While at MIT, Siddiqui was active in many activist causes, including raising awareness on the situation of the Bosnians during the Bosnian Genocide.

Marriage, graduate school, and work
In 1995, she agreed to a marriage arranged by her mother to Karachi-born anesthesiologist Amjad Mohammed Khan just out of medical school and whom she had never seen. The marriage ceremony was conducted over the telephone. Khan then came to the US, and the couple lived first in Lexington, Massachusetts, and then in the Mission Hill neighbourhood of Roxbury, Boston, where he worked as an anesthesiologist at Brigham and Women's Hospital. She gave birth to a son, Muhammad Ahmed, in 1996, and to a daughter, Mariam Bint-e Muhammad, in 1998.

Siddiqui studied cognitive neuroscience at Brandeis University. In early 1999, while she was a graduate student, she taught the General Biology Laboratory course. She received her PhD in 2001 after completing her dissertation on learning through imitation. She co-authored a journal article on selective learning that was published in 2003. One incident that caused controversy was her presentation of a paper on fetal alcohol syndrome, where she concluded that science showed why God had forbidden alcohol in the Quran. When told by some teachers this was inappropriate, she complained bitterly of discrimination to the associate dean of graduate studies, threatening to "open a can of worms".

After receiving her Ph.D., she told one of her advisers she planned to devote herself to her family, rather than a career. She began translating biographies of Arab Afghan shahid (jihad fighters who had been killed) written by Abdullah Yusuf Azzam ("the Godfather of Jihad"). and became more strict in her religion, wearing a niqāb – a black veil that covered everything but her eyes – and avoiding any music – even background music at science exhibits.

In 1999, while living in Boston, Siddiqui founded the Institute of Islamic Research and Teaching as a nonprofit organisation. She was the organisation's president, her husband's treasurer, and her sister's resident agent.[a] She attended a mosque outside the city where she stored copies of the Quran and other Islamic literature for distribution. She also co-founded the Dawa Resource Center, which offered faith-based services to prison inmates.

Divorce, al-Qaeda allegations, and remarriage
Tensions began to arise in her marriage (caused by her overwhelming devotion to activism and jihad according to husband Khan). Siddiqui temporarily moved away from her husband after he threw a baby bottle at her requiring a visit to the emergency room to stitch up her lip. In the summer of 2001, the couple moved to Malden, Massachusetts.

According to her husband Khan, after the 9/11 attacks, Siddiqui was adamant that the family leave the U.S., saying that their lives were in danger if they remained. Once back in Pakistan, Siddiqui demanded that the family move to the border with Afghanistan and Khan work as a medic to help the Taliban mujahideen in their fight against America. Khan was reluctant to disobey his parents who opposed this move, and uncertain if he had reached the stature traditionally thought necessary to wage jihad. Siddiqui agreed to return to him in the U.S. in January 2002 after he agreed to her conditions including that he join her in Islamic activities. She began home-schooling her children.

By this point, the FBI was questioning Siddiqui's former professors and other associates. In May 2002, the FBI began questioning Siddiqui and her husband regarding their purchase over the internet of $10,000 worth of night vision equipment, body armour, and military manuals including The Anarchist's Arsenal, Fugitive, Advanced Fugitive, and How to Make C-4. Khan claimed that these were for hunting and camping expeditions. (He later told authorities he purchased them to please Siddiqui.) The couple made an appointment to talk to the FBI again in a few weeks but Siddiqui insisted the family leave for Pakistan (according to Khan), and on 26 June 2002, the couple and their children returned to Karachi.

In August 2002, Khan alleged that Siddiqui was abusive and manipulative throughout their seven years of marriage; he suspected she was involved in extremist activities. Khan went to Siddiqui's parents' home, announced his intention to divorce her, and argued with her father. Shortly after, Siddiqui's father died of a heart attack, an event blamed on Khan and the marriage difficulties by his ex-in-laws, further poisoning his relations with them.

In September 2002, Siddiqui gave birth to Suleman, the last of their three children. Following an attempted and failed reconciliation and signing of a divorce document shortly after, the couple never met each other again.

The couple's divorce was finalised on 21 October 2002. According to her statements to the FBI, it was at this point that her connections with Al-Qaeda began in earnest.

In February 2003, Siddiqui allegedly married Ammar al-Baluchi, an accused al-Qaeda member and a nephew of al Qaeda leader Khalid Sheikh Mohammed (KSM), in Karachi. While her family denies she married al-Baluchi, Pakistani and US intelligence sources, a psychologist for the defense during her 2009 trial, and Khalid Sheikh Mohammed's family all confirm that the marriage took place.

Alleged conspiring with KSM
Siddiqui left for the US on 25 December 2002, informing her ex-husband Amjad Mohammed Khan that she was looking for a job; she returned on 2 January 2003. He later stated he was suspicious of her explanation as universities were on winter break. The purpose of the trip was to assist Majid Khan in opening a post office box so that it could appear he was living in the US when he mailed his application for an INS travel document. Khan was listed as a co-owner of the box. The FBI alleged that Khan was an al-Qaeda operative. Siddiqui told the FBI that she agreed to open the post box and mail the application because he was a family friend. The P.O. box key was later found in the possession of Uzair Paracha, who was convicted of providing material support to al-Qaeda.

According to the US government, Khan was an operative for an Al-Qaeda cell led by Khalid Sheikh Mohammad which planned to attack targets in the US, in the UK (on Heathrow airport) and inside Pakistan. In the US, C-4 plastic explosives and other chemicals would be smuggled in under the cover of textile exports – 20 and 40 foot (6.1 and 12.2 m) containers filled with women's and children's clothes. The explosives would be used to bomb petrol stations, underground fuel storage tanks in Baltimore and chemicals to poison or destroy pumps to water treatment facilities. A dummy import-export business run by Saifullah Paracha, (now interned at Guantánamo Bay) would import the explosives.

According to the US government, Siddiqui's role was to "rent houses and provide administrative support for the operation". When she returned from Pakistan to the US in January 2003, it was (according to the charge) to help renew the American travel papers of Majid Khan, who would execute the bombing. Khan provided Siddiqui with money, photos and a completed application for an "asylum travel form" that "looked and functioned like a passport", (according to his testimony), and back in the US Siddiqui "opened a post office box in detainee's name, using her driver's licence information".

The plot unraveled after Khan was arrested in Pakistan on 1 March 2003 and sent to Guantánamo. In America, another operative, Uzair Paracha, was arrested in possession of the post box key. According to defense attorneys, testimony gathered by investigators "were likely to have been extracted under conditions of torture." Her lawyer suggested she had been the victim of identity theft, while her sister Fowzia has maintained the post office box was intended for use in applying for jobs at American universities. Charges were not brought against Siddiqui for the opening of the post box or for mailing the application in her trial.

Khan (her ex-husband) was questioned by the FBI and released.

Blood diamond allegations ruled out
According to a dossier prepared by U.N. investigators for the 9/11 Commission in 2004, Siddiqui, using the alias Fahrem or Feriel Shahin, was one of six alleged al-Qaeda members who bought $19 million worth of blood diamonds in Monrovia, Liberia, immediately prior to the 11 September 2001 attacks. The diamonds were purchased because they were untraceable assets to be used for funding al-Qaeda operations. The identification of Siddiqui was made three years after the incident by one of the go-betweens in the Liberian deal. Alan White, former chief investigator of the UN-backed war crimes tribunal in Liberia, said she was the woman. Siddiqui's lawyer maintained credit card receipts and other records showed that she was in Boston at the time.

In early 2003, while Siddiqui was working at Aga Khan University in Karachi, she emailed a former professor at Brandeis and expressed interest in working in the US, citing lack of options in Karachi for women of her academic background.

According to "a combination of US intelligence analysis and direct testimony by at least three senior al-Qaida figures", known as Guantánamo files, Siddiqui was an al-Qaeda operative. The file included evidence from Khalid Sheikh Muhammad, (KSM) the al-Qaeda chief planner of the 11 September 2001 attacks, who was interrogated by the CIA (and subjected to torture (waterboarding) 183 times) after his arrest on 1 March 2003. His "confessions" – obtained while being tortured – triggered a series of related arrests shortly thereafter, and included naming Siddiqui. On 25 March 2003, the FBI issued a global "wanted for questioning" alert for Siddiqui and her ex-husband, Khan. Siddiqui was accused of being a "courier of blood diamonds and a financial fixer for al-Qaida". FBI agent Dennis Lormel, who investigated terrorism financing, said the agency ruled out a specific claim that she had evaluated diamond operations in Liberia, though she remained suspected of money laundering.

Disappearance
On 30 March 2003, she left her parents house along with her three children. According to her parents, she was going to go to Islamabad to visit her uncle but never arrived. WRMEA reported that she and her children were "forcibly removed" and they "disappeared without a trace," with the youngest missing until today. Around 25 March, the FBI put out a "worldwide alert" for Siddiqui and her ex-husband. Siddiqui's mother says that a man on a motorcycle arrived at the family home and told her that if she ever wanted to see her daughter and grandchildren again, she should keep quiet about the whole affair.

Siddiqui's and her children's whereabouts and activities from March 2003 to July 2008 are a matter of dispute. Her supporters and the Pakistani government claim she was held as a prisoner by the U.S.; the U.S. government and others suggest she went into hiding with KSM's al-Baluchi family. Many journalists and witnesses have identified her with "Prisoner 650", a Pakistani woman held captive in Bagram Air Base.

Starting 29 March, a "confusing series" of reports and denials of her arrest and detention appeared in Pakistan and the US. On 1 April 2003, local newspapers reported and Pakistan interior ministry confirmed that a woman had been taken into custody on terrorism charges. NBC also reported that she was in American custody. The Boston Globe described "sketchy" Pakistani news reports saying she had been detained for questioning by Pakistani authorities and the FBI. However, a couple of days later, both the Pakistan government and the FBI publicly stated they were uninvolved in her disappearance. Her sister Fauzia claimed Interior Minister Syed Faisal Saleh Hayat said that her sister had been released and would be returning home "shortly".

Official American Government Narratives
In 2003–2004, the FBI and the Pakistani government said Siddiqui was still at large. On 26 May 2004, US Attorney General John Ashcroft held a press conference described her as among the seven "most wanted" al-Qaeda fugitives and a "clear and present danger to the US". Newsweek reported that she might be "the most immediately threatening suspect in the group".

One day before the announcement, however, The New York Times cited the US Department of Homeland Security saying there were no current risks; American Democrats accused the Bush administration of attempting to divert attention from plummeting poll numbers and to push the failings of the Invasion of Iraq off the front pages.

After her 2008 reappearance and arrest, Siddiqui told the FBI that she had at first gone into hiding with KSM's al Baluchi clan (her lawyer later repudiated that statement) and worked at the Karachi Institute of Technology in 2005, was in Afghanistan in 2007, and also spent time in Quetta, Pakistan, sheltered by various people. She told the FBI she met with Mufti Abu Lubaba Shah Mansoor, and according to the FBI had begun collecting materials on viruses for biological warfare. According to an intelligence official in the Afghan Ministry of the Interior, her son, Ahmed, who was with her when she was arrested, said he and Siddiqui had worked in an office in Pakistan collecting money for poor people. He told Afghan investigators that on 14 August 2008 they had traveled by road from Quetta to Afghanistan. An Afghan intelligence official said he believes that Siddiqui was working with Jaish-e-Mohammed (the "Army of Muhammad"), a Pakistani Islamic mujahideen military group that fights in Kashmir and Afghanistan.

According to her ex-husband Khan, after the global alert for her was issued, Siddiqui went into hiding and worked for al Qaeda. During her disappearance, Khan said he saw her at Islamabad airport in April 2003 as she disembarked from a flight with their son; he said he helped Inter-Services Intelligence identify her. He said he again saw her two years later, in a Karachi traffic jam. Khan unsuccessfully sought custody of his son Ahmed, and said most of the claims of Siddiqui's family in the Pakistani media relating to her and their children were one-sided and largely false.

In a signed affidavit, Siddiqui's maternal uncle, Shams ul-Hassan Faruqi, stated that on 22 January 2008 she visited him in Islamabad and told him she had been held by Pakistani agencies. Knowing he had worked in Afghanistan and made contact with the Taliban in 1999, she asked for his help to cross into Taliban-controlled Afghanistan where she thought she would be safe. He told her he was no longer in touch with them. He notified his sister, Siddiqui's mother, who came the next day to see her daughter. He said that Siddiqui stayed with them for two days. Investigating the disappearance, U.S. journalist Deborah Scroggins reported that Geo TV presenter Hamid Mir informed her, that friends of Siddiqui believed she had gone underground to evade the FBI. Scroggins was also warned by Pakistanis with jihadist connections (including Khalid Khawaja) that she (Scroggins) might end up like Daniel Pearl (beheaded) if she attempted to pursue finding Siddiqui.

The U.S. government claimed it had not held Siddiqui during the time frame and was unaware of her location from March 2003 until July 2008. The mass of secret U.S. cables released in 2010 by Wikileaks included memos by the U.S. embassy in Islamabad, Pakistan, asking other U.S. government departments whether Asfia had been in secret custody. One stated: "Bagram officials have assured us that they have not been holding Siddiqui for the last four years, as has been alleged."

The U.S. ambassador to Pakistan, Anne W. Patterson, stated that Siddiqui had not been in US custody "at any time" prior to July 2008. The US Justice Department and the CIA denied the allegations, and Gregory Sullivan, a State Department spokesman, said: "For several years, we have had no information regarding her whereabouts whatsoever. It is our belief that she ... has all this time been concealed from the public view by her own choosing." Assistant U.S. Attorney David Raskin said in 2008 that US agencies found "zero evidence" that she was abducted, kidnapped, or tortured in 2003. He added: "A more plausible inference is that she went into hiding because people around her started to get arrested, and at least two of those people ended up at Guantanamo Bay." According to some U.S. officials, she went underground after the FBI alert for her was issued, and was at large working on behalf of al-Qaeda. The Guardian cited an anonymous senior Pakistani official suggesting Siddiqui may have abandoned the militant cause.

Narratives about Kidnapping and Captivity
When Siddiqui's ex-mother and father-in-law filed a custody suit against the Siddiqui family in an attempt to see their grandchildren (the Siddiqui family refused to talk to them), Siddiqui's mother claimed under oath the FBI and US Justice Department officials had informed her that "the minors are with the mother and are in safe condition," the opposite of what such officials had told her American lawyer in May of that year. Siddiqui's sister and mother denied that she had any connections to al Qaeda and claimed that the U.S. held her secretly in Afghanistan. They pointed to comments by former Bagram Air Base, Afghanistan, detainees who say Siddiqui had been at the prison while they were there. Her sister said that Siddiqui had been raped, and tortured for five years. According to journalist, Muslim convert, and former Taliban captive Yvonne Ridley, Siddiqui spent those years in solitary confinement at Bagram as "Prisoner 650". Six human rights groups, including Amnesty International, listed her as a possible ghost prisoner held by the US. In early 2007, the Pakistan government started releasing more than a hundred people who had been listed as "missing" (the CIA reportedly detained up to 100 people at secret facilities.) S.H. Faruqi, Siddiqui's uncle, reported that Siddiqui visited him in January 2008, telling him she had been imprisoned and tortured at Bagram Airfield for several years and released to serve as a double agent, infiltrating extremist groups. Siddiqui herself later claimed that she had been kidnapped by U.S. intelligence and Pakistani intelligence.

According to one Pakistani report, her mother claimed to have been warned by an unidentified man "not to make a fuss about her daughter's disappearance, if she wants safe recovery of her daughter", suggesting that either government intelligence services or the "nexus of Pakistani and Arab jihadis" had hidden Siddiqui.

In 2008, four men that escaped captivity mentioned in a series of interviews about a Pakistani woman (known only as "Prisoner 650") who was routinely tortured at the prison, whom they identified as Siddiqui.

Another theory was that the CIA and FBI did not have the ability to capture suspects in Pakistan (where most people were passionately anti-American), only the ISI had the ability to capture Siddiqui, and while they may have known how to get her or even have her in custody, they were not "ready to hand her over", whatever reward the Americans offered.

Reappearance of Her Children
Siddiqui has not explained clearly what happened to her other two children. An FBI agent claims that she said that pursuing the cause of jihad had to take priority. Khan said he believed that the missing children were in Karachi, either with or in contact with Siddiqui's family, and not in US detention. He said that they were seen in her sister's house in Karachi and in Islamabad since 2003.

Ahmed and Siddiqui reappeared in 2008. Afghan authorities handed the boy over to his aunt in Pakistan in September 2008, who has prohibited the press from talking to him.

In April 2010, Mariam was found outside the family house wearing a collar with the address of the family home. She was said to be speaking English. A Pakistani ministry official said the girl was believed to have been held captive in Afghanistan from 2003 to 2010. DNA confirmed her as Siddiqui's.

Her youngest child remains missing since 2003, when she was allegedly kidnapped.

Alleged danger
Siddiqui was on the CIA's list of suspected al-Qaeda terrorists it was authorized to "kill or capture". According to Rolf Mowqatt-Larssen of the Counterterrorism Center at the CIA, what set Siddiqui apart from other terrorism suspects was

"her combination of high intelligence (including general scientific know-how), religious zeal, and years of experience in the United States".
"So far they have had very few people who have been able to come to the U.S. and thrive. Aafia is different. She knows about U.S. immigration procedures and visas. She knows how to enroll in American educational institutions. She can open bank accounts and transfer money. She knows how things work here. She could have been very useful to them simply for her understanding of the U.S."
While the CIA's sources of information could not determine her exact role in al Qaeda, "[s]he was always in the picture. Connections between her and other people in FBI was looking at surfaced in just about every al-Qaeda investigation with a U.S. angle. She was always on our radar."

According to the FBI, in her testimony to them she had collected materials on viruses for biological warfare and one of her projects was finding a way to infect America's poultry supplies with an antibody that would allow chickens to pass salmonella on to humans more easily. (She later destroyed her work after suspecting Abu Lubab was hoping to double cross her and turn into the United States authorities.

Arrest in Afghanistan
On the evening of 17 July 2008, a woman was approached by Ghazni Province police officers in the city of Ghazni outside the Ghazni governor's compound. She was holding two small bags at her side while crouching on the ground. This aroused the officer's suspicion, raising concerns that she might be concealing a bomb under her burqa. Previously, a shopkeeper had noticed a woman in a burqa drawing a map, which is suspicious in Afghanistan where women are generally illiterate. There had also been a report that a Pakistani woman in a burqa with a boy were traveling in Afghanistan urging women to volunteer for suicide bombing. She said her name was Saliha, that she was from Multan in Pakistan, and that the boy's name was Ali Hassan. Discovering that she did not speak either of Afghanistan's main languages, Pashtu or Dari, the officers regarded her as suspicious. She told the police she was looking for her husband, needed no help, and started to walk away. She was arrested and taken to the police station for questioning. She initially claimed the boy was her stepson, Ali Hassan (The woman was not identified as Siddiqui until after hospitalized and fingerprinted). She subsequently admitted he was her biological son when DNA testing proved the boy to be Ahmed.

In a bag she was carrying, the police found a number of documents in English and Urdu describing how to make explosives, chemical weapons, Ebola, dirty bombs, and radiological agents (which discussed the mortality rates of certain weapons), and handwritten notes referring to a "mass casualty attack" that listed various U.S. locations and landmarks (including the Plum Island Animal Disease Center, the Empire State Building, the Statue of Liberty, Wall Street, the Brooklyn Bridge, and the New York City subway system), according to her indictment. The Globe also mentioned one document about a "theoretical" biological weapon that did not harm children. She also reportedly had documents about American military bases, excerpts from a bombmaking manual, a one-gigabyte digital media storage device that contained over 500 electronic documents (including correspondence referring to attacks by "cells", describing the U.S. as an enemy, and discussing recruitment of jihadists and training), maps of Ghazni and the provincial governor's compounds and nearby mosques, and photos of members of the Pakistani military. Other notes described various ways to attack enemies, including by destroying reconnaissance drones, using underwater bombs, and using gliders.

She also had "numerous chemical substances in gel and liquid form that were sealed in bottles and glass jars", according to the later complaint against her, and about two pounds of sodium cyanide, a highly toxic poison. U.S. prosecutors later said that sodium cyanide is lethal even when ingested in small doses (even less than five milligrams), and various of the other chemicals she had could be used in explosives. Abdul Ghani, Ghazni's deputy police chief, said she later confessed she had planned a suicide attack against the governor of Ghazni Province.

Explanation of visit
Attempting to explain the timing of her January 2008 visit to her uncle and asking for help in contacting the Taliban in Afghanistan, and her reappearance in Ghazni in July later that year, journalist Deborah Scroggins noted that a breakdown in the "long-standing alliance between the Deobandi jihadis and the military" occurred in preceding months, which – if Siddiqui was in hiding rather than imprisoned – could have led to Siddiqui's "falling out with her secret government protectors". In 2007, a roving "burka brigade" of women based at Lal Mosque attempted to enforce sharia law in Islamabad. Attempts to stop them climaxed in July when at least 100 militants were killed by the military in the storming of the Lal Mosque. In the next five months, dozens of suicide attacks killing almost 2,000 people (including many soldiers) were executed in retaliation. Scroggins believed this bloodshed may have alienated any military protection Siddiqui had, and the role played by women of the "burka brigade" could have been seen by conservative Islamists as evidence of women causing fitna (strife).

On the other hand, supporters noted that Siddiqui's reappearance "loitering in Ghazni ... less than two weeks" after a press conference by Yvonne Ridley where Ridley alleged Siddiqui had been "held in isolation by the Americans for more than four years", and which "attracted enormous coverage" especially in the Muslim world, seemed highly suspicious.

Shooting(s) in Ghazni
There are conflicting accounts of the events following her arrest in Ghazni.

Official American Narrative
American authorities said that two FBI agents, a US Army warrant officer, a US Army captain, and their US military interpreters arrived in Ghazni the following day on 18 July to interview Siddiqui at the Afghan National Police facility where she was being held. They reported they congregated in a meeting room that was partitioned by a curtain, but did not realise that Siddiqui was standing unsecured behind the curtain. The warrant officer sat down and put his loaded M4 carbine on the floor by his feet near the curtain. Siddiqui drew back the curtain, picked up the rifle, and pointed it at the captain. "I could see the barrel of the rifle, the inner portion of the barrel of the weapon; that indicated to me that it was pointed straight at my head," he said. Then, she was said to have threatened them loudly in English, and yelled "Get the fuck out of here" and "May the blood of [unintelligible] be on your [head or hands]". The captain dived for cover to his left as she yelled "Allah Akbar" and fired at least two shots at them, missing them. An Afghan interpreter who was seated closest to her tried to disarm her. At that point the warrant officer returned fire with a 9 millimeter pistol, hitting her in the torso, and one of the interpreters disarmed her. A Justice Department statement said that Siddiqui struck and kicked the officers during the ensuing struggle; "she shout[ed] in English that she wanted to kill Americans" and then lost consciousness.

Dr. Aafia's Narrative
Siddiqui related a different version of events, according to Pakistani senators who later visited her in jail. She denied touching a gun, shouting, or threatening anyone. She said she was beaten and fell asleep in her bed, and then heard voices in the room. She said she stood up to see who was on the other side of the curtain, and that after one of the startled soldiers shouted "She is loose", she was shot. On regaining consciousness, she said someone said "We could lose our jobs."

Additional Narratives
Some of the Afghan police offered a third version of the events, telling Reuters that US troops had demanded that she be handed over, disarmed the Afghans when they refused, and then shot Siddiqui mistakenly thinking she was a suicide bomber.

Hospital treatment and evaluation
Siddiqui was taken to U.S. military base Bagram Airfield in Afghanistan by helicopter in critical condition. When she arrived at the hospital she was rated at level 3 on the Glasgow Coma Scale, but she underwent surgery without complication. She was hospitalised at the Craig Theater Joint Hospital, and recovered over the next two weeks. According to FBI reports prepared after the operation, Siddiqui repeatedly denied shooting anyone. FBI reports maintained that Siddiqui told a U.S. special agent at the Craig Hospital on or about 1 August that "spewing bullets at soldiers is bad," and expressed surprise that she was being treated well.

While at the hospital she was interrogated by an FBI agent every day for ten days for an "average of eight hours" a day. Her testimony was at odds with what Siddiqui later told lawyers and the court about what happened during her disappearance. Supporters complained that she was not given a Miranda warning, nor did she have access to a Pakistani consular official, and that she was in a "narcotic state" at the time. She later told visiting Pakistani her statements might not look good to the Pakistani public but she had made them because her children had been threatened.

Criminal complaint and trial
In pretrial activity, defense attorney Elaine Sharp said that the documents and item found on Siddiqui were planted. A government terrorism expert disagreed, stating there were "hundred of pages in her own handwriting". In Pakistan, Siddiqui's sister Fowzi accused the U.S. of raping and torturing her sister, and of denying her medical treatment. The Pakistan National Assembly passed a unanimous resolution calling for Siddiqui's repatriation.

Prior to her trial, Siddiqui said she was innocent of all charges. She maintained she could prove she was innocent but refused to do so in court. On 11 January 2010, Siddiqui told the judge that she would not co-operate with her attorneys and wanted to fire them. She said she did not trust the judge and added, "I'm boycotting the trial, just to let all of you know. There's too many injustices." She then put her head down on the defence table as the prosecution proceeded.

Charges
On 31 July 2008, while Siddiqui was still being treated in Afghanistan, she was charged in a sealed criminal complaint in the United States District Court for the Southern District of New York with assault with a deadly weapon and with attempting to kill a United States Army Captain "while engaged in ... official duties." In total, she was charged on two counts of attempted murder of US nationals, officers, and employees, assault with a deadly weapon, carrying and using a firearm, and three counts of assault on US officers and employees.

Explaining why the U.S. may have chosen to charge her as they did rather than for her alleged terrorism, Bruce Hoffman, professor of security studies at Georgetown University, said, "There's no intelligence data that needs to be introduced, no sources and methods that need to be risked. It's a good old-fashioned crime; it's the equivalent of a 1920s gangster with a tommy gun."

Defense lawyer Sharp expressed scepticism regarding both the terrorism and assault charges: "I think it's interesting that they make all these allegations about the dirty bombs and other items she supposedly had, but they haven't charged her with anything relating to terrorism ... I would urge people to consider her as innocent unless the government proves otherwise."

Extradition and arraignment
On 4 August 2008, Siddiqui was placed on an FBI jet and flown to New York City after the Afghan government granted extradition to the United States for trial. She refused to appear for her arraignment or attend a hearing in September or meet with visitors. Siddiqui made her first appearance before a judge in a Manhattan courtroom on 6 August 2008 following which she was remanded into custody.

Medical treatment and psychological assessments
On 11 August, after her counsel maintained that Siddiqui had not seen a doctor since arriving in the U.S. the previous week, US Magistrate Judge Henry B. Pitman ordered that she be examined by a medical doctor within 24 hours. Prosecutors maintained that Siddiqui had received adequate medical care for her gunshot wound but could not confirm whether she had been seen by a doctor or paramedic. The judge postponed her bail hearing until 3 September. An examination by a doctor the following day found no visible signs of infection; she also received a CAT scan.

In September 2008, a prosecutor reported to the court that Siddiqui had refused to be examined by a female doctor, despite the doctor's extensive efforts. In November 2008, forensic psychologist Leslie Powers reported that Siddiqui had been "reluctant to allow medical staff to treat her". Her last medical exam had indicated her external wounds no longer required medical dressing and were healing well.

Siddiqui's trial was subject to delays, the longest being six months to perform psychiatric evaluations. She had been given routine mental health check-ups ten times in August and six times in September. She underwent three sets of psychological assessments before trial. Her first psychiatric evaluation diagnosed her with depressive psychosis, and her second evaluation, ordered by the court, revealed chronic depression. Leslie Powers initially determined Siddiqui mentally unfit to stand trial. After reviewing portions of FBI reports, however, she told the pre-trial judge she believed Siddiqui was faking mental illness.

In a third set of psychological assessments, more detailed than the previous two, three of four psychiatrists concluded that she was "malingering" (faking her symptoms of mental illness) and that she behaved normally when she thought the assessors were not looking. One suggested that this was to prevent criminal prosecution and to improve her chances of being returned to Pakistan. In April 2009, Manhattan federal judge Richard Berman held that she "may have some mental health issues" but was competent to stand trial.

While Khalid Sheikh Mohammad and other ghost prisoners had given the Red Cross "elaborate descriptions of waterboardings and other tortures" they had suffered, government psychiatrist Sally Johnson testified in a pre-trial hearing that Siddiqui had never given anyone, whether her brother, her lawyers, Pakistani senators, or embassy personnel, other visitors, prison staff, or psychiatrists, "a clear account of any torture or imprisonment".

Antisemitism
A three-person defence team was hired by the Pakistani embassy to supplement her two existing public defenders, but Siddiqui refused to co-operate with them. She tried to dismiss her lawyers on the grounds that they were Jewish. She said the case against her was a Jewish conspiracy, demanded that no Jews be allowed on the jury, and that all prospective jurors be DNA-tested and excluded from the jury at her trial "if they have a Zionist or Israeli background." She stated: "They are all mad at me ... I have a feeling everyone here is them – subject to genetic testing. They should be excluded, if you want to be fair." In regard to her comments, Siddiqui's legal team stated that her incarceration had damaged her mind.
While at Federal Medical Center, Carswell, she wrote a letter to the warden to give to President Obama, asserting, "Study the history of the Jews. They have always back-stabbed everyone who has taken pity on them and made the 'fatal' error of giving them shelter. ... and it is this cruel, ungrateful back-stabbing of the Jews that has caused them to be mercilessly expelled from wherever they gain strength. This why 'holocausts' keep happening to them repeatedly! If they would only learn to be grateful and change their behavior!! ..."

She later claimed she was not against all "Israeli Americans". After her sentence in the case of her shooting US troops was given, she reportedly reacted by:

Holding her right index finger in the air, she said: “This is a verdict coming from Israel and not from America. That’s where the anger belongs.”

Trial proceedings
After 18 months of detention, Siddiqui's trial began in New York City on 19 January 2010. Prior to the jury entering the courtroom, Siddiqui told onlookers that she would not work with her lawyers because the trial was a sham. She also said: "I have information about attacks, more than 9/11! ... I want to help the President to end this group, to finish them ... They are a domestic, U.S. group; they are not Muslim."

Nine government witnesses were called by the prosecution. Army Captain Robert Snyder, John Threadcraft, a former army officer, and FBI agent John Jefferson testified first. As Snyder testified that Siddiqui had been arrested with a handwritten note outlining plans to attack various US sites, she interjected:

The court also heard from FBI agent John Jefferson and Ahmed Gul, an army interpreter, who recounted their struggle with her. The judge disallowed as evidence her possession of chemicals and terror manuals and her alleged ties to al Qaeda because they could have created an inappropriate bias.

Her defence argued that there was no forensic evidence that the rifle was fired in the interrogation room. They noted the nine government witnesses offered conflicting accounts of how many people were in the room, where they were positioned and how many shots were fired. It said that her handbag contents were not credible as evidence because they were sloppily handled. The prosecution argued that it was not unusual to fail to get fingerprints off a gun. "This is a crime that was committed in a war zone, a chaotic and uncontrolled environment 6,000 miles away from here." Gul's testimony appeared, according to the defence, to differ from that given by Snyder with regard to whether Siddiqui was standing or on her knees as she fired the rifle. When Siddiqui testified, she admitted trying to escape, but said she had not taken the rifle or fired any shots. She said she had been "tortured in secret prisons" before her arrest by a "group of people pretending to be Americans, doing bad things in America's name".

Siddiqui insisted on testifying at the trial against the advice of her lawyers. According to at least one source (Deborah Scroggins), Siddiqui "avoided the question of where she had been for the last five years" and her replies under cross examination may have damaged her credibility in jurists' eyes. In answer to prosecutor's questions she stated that the documents in her bag on terror plans and weapons had been given to her, and that she did not know that the boy who was with her in Ghazni was her son. When it was pointed out that the documents in her bag were in her own handwriting, she stated "in a vague and halting manner" that she had been forced to copy them out of a magazine so that her children would not be tortured. When questioned about taking a firearms course she stated that "everyone used to take it". The pistol safety instructor then testified that he remembered teaching her how to fire "hundreds of rounds". In his closing arguments the prosecutor told the jury that Siddiqui had "raised her right hand" and "lied to your face".

During the trial, Siddiqui was removed from the court several times for repeatedly interrupting the proceedings with shouting; on being ejected, she was told by the judge that she could watch the proceedings on closed-circuit television in an adjacent holding cell. A request by the defence lawyers to declare a mistrial was turned down by the judge. Amnesty International monitored the trial for fairness.

Conviction
The trial lasted 14 days with the jury deliberating for three days before reaching a verdict. On 3 February 2010, Siddiqui was found guilty of two counts of attempted murder, armed assault, using and carrying a firearm, and three counts of assault on US officers and employees. After jurors found Siddiqui guilty, she exclaimed: "This is a verdict coming from Israel, not America. That's where the anger belongs."

She faced a minimum sentence of 30 years and a maximum of life in prison on the firearm charge, and could also have received a sentence of up to 20 years for each attempted murder and armed assault charge, and up to 8 years on each of the remaining assault counts. Her lawyers requested a 12-year sentence, instead of the life sentence recommended by the probation office. They argued that mental illness drove her actions when she attempted to escape from the Afghan National Police station "by any means available ... what she viewed as a horrific fate". Her lawyers also claimed her mental illness was on display during her trial outbursts and boycotts, and that she was "first and foremost" the victim of her own irrational behaviour. The sentencing hearing set to take place on 6 May 2010 was rescheduled for mid-August 2010 and then September 2010.

Sentencing
Siddiqui was sentenced to 86 years in prison by Judge Berman on 23 September 2010. During the sentencing hearing, which lasted one hour, Siddiqui spoke on her own behalf. Upon hearing the verdict, she turned to trial spectators and told them that "this verdict coming from Israel and not from America".

A New York Times reporter wrote that at times during the hearing Judge Berman seemed to be speaking to an audience beyond the courtroom, in an apparent attempt to address widespread speculation about Siddiqui and her case. He gave as an example a reference to the five-year period before her 2008 arrest of Siddiqui's disappearance and claims of torture, where the judge said:

At the time of sentencing Siddiqui did not show any interest in filing an appeal, instead saying "I appeal to God and he hears me." After she was sentenced, she urged forgiveness and asked the public not to take any action in retaliation. She stated, "forgive everybody in my case, please ... Don't get angry. If I'm not angry, why should anyone else be?" In a notably gracious exchange between the bestower and recipient of an 80+ year sentence of incarceration, the judge wished her "the very best going forward", and both Siddiqui and the judge thanked each other.

Imprisonment
Siddiqui (Federal Bureau of Prisons #90279-054) was originally held at Metropolitan Detention Center, Brooklyn. She is now being held in Federal Medical Center, Carswell in Fort Worth, Texas, a federal prison for female inmates with special mental health needs, and also relatively close to the home of her brother Ali Siddiqui. Her release date is 7 May 2082.

In July 2019, while visiting Washington, DC, Pakistani Prime Minister Imran Khan suggested Siddiqui should be exchanged for Shakil Afridi, a Pakistani doctor accused of helping the Americans confirm the identity of Osama bin Laden, in advance of the raid where he was killed.

Children
Siddiqui's son Ahmed was released from Afghanistan to the custody of his aunt in Pakistan following enormous outcry from the Pakistani public and politicians. While Pakistani law would normally give his father custody, his father did not want to fight the passionate public opinion supporting his aunt Fowzia. Ahmed now lives in Karachi with his aunt, who has prohibited him from talking to the press. In April 2010, Pakistan Interior Minister Rehman Malik claimed a 12-year-old girl found outside a house in Karachi was identified using DNA as Siddiqui's daughter, Mariyam, and that she had been returned to her family. Their father and his parents have not been allowed by the aunt to see either child.

Reactions
Attacks, threats, and exchange offers
For al Qaeda and Pakistani jihadi groups, Siddiqui's case became a "rallying cry", and they joined in accusing the Pakistani government and military of failing to protect and avenge her.

According to a video released by Hakimullah Mehsud, head of the TTP (Tehreek e Taliban Pakistan) at the time, the 2009 Camp Chapman attack in Afghanistan that killed seven CIA officers was partly in revenge for Aafia's imprisonment. The 2010 Times Square car bombing attempt occurred one day after Mehsud released another video promising to avenge Siddiqui. The perpetrator of the attempt was Faisal Shahzad, a recently naturalized Pakistan-born citizen who had contacts with Jaish-e-Muhammad and Hakimullah Mehsud.

According to a February 2010 report in the Pakistani newspaper The News International, the Taliban threatened to execute U.S. soldier Bowe Bergdahl, whom they had captured on 30 June 2009 in retaliation for Siddiqui's conviction. A Taliban spokesperson claimed that members of Siddiqui's family had requested help from the Taliban to obtain her release from prison in the U.S. Bergdahl was released on 31 May 2014 in exchange for five Guantanamo Bay detainees.

In September 2010, the Taliban kidnapped Linda Norgrove, a Scottish aid worker in Afghanistan, and Taliban commanders insisted Norgrove would be handed over only in exchange for Siddiqui. On 8 October 2010, Norgrove was accidentally killed during a rescue attempt, by a grenade thrown by one of her rescuers.

In July 2011, then-deputy of the Tehrik-i-Taliban Pakistan, Waliur Rehman, announced that they wanted to swap Siddiqui for two Swiss citizens abducted in Balochistan. The Swiss couple escaped in March 2012.

In December 2011, al-Qaeda leader Ayman al-Zawahiri demanded the release of Siddiqui in exchange for Warren Weinstein, an American aid worker kidnapped in Pakistan on 13 August 2011. Weinstein was accidentally killed in a drone strike in January 2015.

In January 2013, al-Qaeda-linked terrorists involved in the Algerian In Amenas hostage crisis listed the release of Siddiqui as one of their demands.

In June 2013, the captors of two Czech women kidnapped in Pakistan demanded the release of Siddiqui in exchange for the two captives. Both Czech women were released in March 2015, following intense negotiations by a Turkish NGO IHH.

In August 2014, it was reported that the terrorist who claimed responsibility for the beheading of U.S. photojournalist James Foley mentioned Siddiqui in an email to Foley's family. Siddiqui was identified in the email as one of the Muslim "sisters" the Islamic State was purportedly willing to swap as part of a prisoner exchange with the United States.

In February 2015, Paul Gosar said the family of Kayla Mueller had been told plans to swap her for Siddiqui were underway in the months before her death. ISIS had also demanded $6.6 million in exchange for Mueller.

In March 2017, Al-Qaeda in the Arabian Peninsula leader Qasim al-Raymi said that his group demanded the release of Siddiqui in exchange for Luke Somers, an American journalist kidnapped in Yemen in September 2013. Somers was killed during a rescue attempt in December 2014.

In January 2022, Malik Faisal Akram, a 44-year-old British national, took hostages at the Beth Israel synagogue in Colleyville, Texas, near where she is imprisoned, and demanded her release. During the hostage taking, Siddiqui's attorney said

Faizan Syed, executive director of the Dallas-Fort Worth chapter of the Council on American-Islamic Relations, who had campaigned for Siddiqui's Release arguing that she was a political prisoner who was wrongly accused through false evidence, has also condemned the hostage-taking, calling it wrong, heinous and "something that is completely undermining our efforts to get Dr. Aaifa released."

Pakistan
The case was covered very differently in Pakistan than in the United States.

After Siddiqui's conviction, she sent a message through her lawyer, saying that she does not want "violent protests or violent reprisals in Pakistan over this verdict." Thousands of students, political and social activists protested in Pakistan. Some shouted anti-American slogans, while burning the American flag and effigies of President Barack Obama in the streets. Her sister has spoken frequently and passionately on her behalf at rallies. Echoing her family's comments and anti-US sentiment, many believe she was detained in Karachi in 2003, held at the US Bagram Airbase and tortured, and that the charges against her were fabricated.

In August 2009, Pakistani Prime Minister Yusuf Raza Gilani met with Siddiqui's sister at his residence and assured her that Pakistan would seek Siddiqui's release from the US. The Pakistani government paid $2 million for the services of three lawyers to assist in the defense of Siddiqui during her trial. Many Siddiqui supporters were present during the proceedings, and outside the court dozens of people rallied to demand her release.

Her conviction was followed with expressions of support by many Pakistanis, who appeared increasingly anti-American, as well as by politicians and the news media, who characterised her as a symbol of victimisation by the United States. Graffiti "Free Dr. Aafia" appeared "even in remote areas" of the country.

The Pakistani Embassy in Washington, D.C., expressed its dismay over the verdict, which followed "intense diplomatic and legal efforts on her behalf. [We] will consult the family of Dr. Aafia Siddiqui and the team of defence lawyers to determine the future course of action." Prime Minister Gilani described Siddiqui as a "daughter of the nation," and opposition leader Nawaz Sharif promised to push for her release. On 18 February, President Asif Ali Zardari requested of Richard Holbrooke, U.S. Special Envoy to Afghanistan and Pakistan, that the U.S. consider repatriating Siddiqui to Pakistan under the Pakistan-U.S. Prisoner Exchange Agreement. On 22 February, the Pakistani Senate urged the government to work towards her immediate release. Shireen Mazari, editor of the Pakistani newspaper The Nation, wrote that the verdict "did not really surprise anyone familiar with the vindictive mindset of the U.S. public post-9/11".

In September 2010, Pakistan Interior Minister Rehman Malik sent a letter to the United States Attorney General calling for repatriation of Siddiqui to Pakistan. He said that the case of Siddiqui had become a matter of public concern in Pakistan and her repatriation would create goodwill for the US.

A few Pakistanis questioned the outpouring of support. Her ex-husband said Siddiqui was "reaping the fruit of her own decision. Her family has been portraying Aafia as a victim. We would like the truth to come out." Shakil Chaudhry lamented the "mass hysteria" of supporters. But when one columnist (Mubashir Lucman) raised questions about Asfia's sister Fowzia's account, graffiti "appeared all over Karachi insulting" him.

US observers noted the Pakistani reaction. Jessica Eve Stern, a terrorism specialist and lecturer at Harvard Law School, observed: "Whatever the truth is, this case is of great political importance because of how people [in Pakistan] view her." Foreign Policy reported that unsubstantiated rumours, widely repeated in the Pakistani press, that she had been sexually abused by her captors had "become part of the legend that surrounds her, so much so that they are repeated as established facts by her supporters, who have helped build her iconic status" as a folk hero. According to the New York Times,

Journalist Scroggins complained about the lack of curiosity and investigation by Pakistani public and press of a number of questions about the case – how Siddiqui's daughter Maryam turned up at her grandmother's house and where she had been, what connection the "Karachi Institute of Technology", and the cleric Abu Lubaba had had with Siddiqui. She noted that while thousands of Pakistanis had been killed by bomb and assassinations in tribal areas, in contrast to the rage against the U.S., no rallies were held in protest of jihadi attacks (Scroggins argued) because Pakistanis were fearful of them.