Aafia Siddiqui

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.

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.

Five years later, she reappeared in Ghazni, Afghanistan, so was arrested by Afghan police and held for questioning by the FBI. While in custody, Siddiqui told the FBI she had gone into hiding but later disavowed her testimony and stated she had been abducted and imprisoned. Supporters believe she was held captive at Bagram Air Force Base as a ghost prisoner—charges the US government denies.

After receiving her PhD, 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.

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.

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.

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 Aafia. She noted that while thousands of Pakistanis had been killed by bomb and assassinations in tribal areas, in contrast to the rage against the US, no rallies were held in protest of jihadi attacks (Scroggins argued) because Pakistanis were fearful of them.

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 ft foot 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.

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 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.

While in custody in Ghazni, police found documents and notes for making bombs along with containers of sodium cyanide in her possession. During the second day in custody, she shot at visiting U.S. FBI and Army personnel with an M4 carbine one of the interrogators had placed on the floor by his feet. She was shot in the torso when the warrant officer returned fire with a 9-millimeter pistol. She was hospitalized, and treated; then extradited and flown to the US where in September 2008 she was indicted on charges of assault and attempted murder of a US soldier in the police station in Ghazni—charges she denied. She was convicted on 3 February 2010 and later sentenced to 86 years in prison.

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's 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. After receiving psychological evaluations and therapy, the judge 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.

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.

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.

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."

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.

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".

Siddiqui's son Ahmed was released from Afghanistan to 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 Fawzia. He now lives with his aunt in Karachi, 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 by DNA as Siddiqui's daughter, Mariyam, and that she had been returned to her family. Their father and his parents have not been allowed to see either child.

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 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.

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.

According to a video released by Hakimullah Mehsud, head of the Taliban 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 US 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 US. Bergdahl was released on 31 May 2014 in exchange for five Guantanamo Bay detainees.

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.

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.

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, a US journalist (Deborah Scroggins) reported that Geo TV presenter Hamid Mir informed her that friends of Siddiqui believed she had gone underground avoiding 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.

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, DNA identified a girl as Siddiqui's daughter, Mariyam.

The US 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 US 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.

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 was accompanied by a young boy that she said was her adopted son. 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.

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 2000 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 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.

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.

Siddiqui was provided care for her wound while incarcerated in the US. 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. On 9 September 2008, she underwent a forced medical exam. 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. A psychiatrist employed by the prosecutor to examine Siddiqui's competence to stand trial, Gregory B. Saathoff, noted in a March 2009 report that Siddiqui frequently verbally and physically refused to allow the medical staff to check her vital signs and weight, attempted to refuse medical care once it was apparent that her wound had largely healed, and refused to take antibiotics. At the same time, Siddiqui claimed to her brother that when she needed medical treatment she did not get it, which Saathoff said he found no support for in his review of documents and interviews with medical and security personnel, nor in his interviews with Siddiqui.

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: "I am aware of no evidence in the record to substantiate these allegations or to establish them as fact. There is no credible evidence in the record that the United States officials and/or agencies detained Dr. Siddiqui".

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 US 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 US intelligence and Pakistani intelligence.

In May 2004, the FBI named Siddiqui as one of its seven Most Wanted Terrorists. 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.

In 2003–04, 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".

In February 2003, Siddiqui 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.

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. Defense attorneys note that 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.

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.

Aware that the FBI wanted her for questioning, she left her parents' house 30 March 2003 with her three children. According to her parents, she was going to go to Islamabad to visit her uncle but never arrived. Around 25 March, the FBI put out a "worldwide alert" for Aafia and her ex-husband.

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 US; the US government and others (including Suddiqui in her statements to the FBI immediately after her arrest) suggest she went into hiding with KSM's al-Baluchi family.

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. 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".

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.

Siddiqui has not explained clearly what happened to her other two children. According to a psychiatric exam given while she was in custody, her story has alternated between claiming that the two youngest children were dead and that they were with her sister Fowzia. She told one FBI agent 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.

The US government said it had not held Siddiqui during that 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 US Embassy in Islamabad Pakistan asking other US 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."

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.

According to her husband Khan, after the 11 September attacks, Siddiqui was adamant that the family leave the US, 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 US 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 Aafia'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.

Siddiqui left for the US on 25 December 2002, informing her ex-husband Amjad that she was looking for a job; she returned on 2 January 2003. Amjad 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.

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 her husband threw a baby bottle at her and she had to be taken to the emergency room to stitch up her lip. In the summer of 2001, the couple moved to Malden, Massachusetts.

According to a dossier prepared by UN 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.

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.

There is no doubt that the case of an ultraconservative, educated middle-class Pakistani woman who shunned the ways of the West and defied America has resonated with the Pakistani public. ... All of this has taken place with little national soul-searching about the contradictory and frequently damning circumstances surrounding Ms. Siddiqui, who is suspected of having had links to Al Qaeda and the banned jihadi group Jaish-e-Muhammad. Instead, the Pakistani news media have broadly portrayed her trial as a "farce", and an example of the injustices meted out to Muslims by the United States since 11 Sept. 2001.

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; Separating the Components of 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".

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. 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.

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.

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. Journalist Deborah Scroggins suggested that through the association's contacts Siddiqui may have been drawn into the world of terrorism:

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.

Siddiqui was born in Pakistan to a Deobandi Muslim family. In 1990, she went to study in the United States and obtained a PhD 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. After his arrest and interrogation under torture Khalid Sheikh Muhammad allegedly 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. Around this time she and her three children disappeared in Pakistan.

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 Masters and her PhD 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, doing charity work, and urging support for jihad in Muslim countries such as Afghanistan and Bosnia. 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 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.

Siddiqui moved to Houston, Texas, US 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.

Aafia Siddiqui (Urdu: عافیہ صدیقی ‎; born 2 March 1972) is a Pakistani neuroscientist with degrees from MIT and Brandeis University, who was convicted of multiple felonies. In 2010, she was convicted of seven counts of attempted murder and assault of US personnel, and is serving her 86-year sentence at the Federal Medical Center, Carswell in Fort Worth, Texas.

Explaining why the US 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."