[26] Her support for strict Islam in the face of feminist opposition to his Hudood Ordinances drew the attention of General Muhammad Zia-ul-Haq who appointed her to a Zakat Council.

Al Kifah included members who assassinated Jewish ultranationalist Meir Kahane and helped Ramzi Yousef with the 1993 World Trade Center bombing.

[1] Journalist Deborah Scroggins suggested that through the association's contacts Siddiqui may have been drawn into the world of terrorism: At MIT, several of the MSA's most active members had fallen under the spell of Abdullah Azzam, a Muslim Brother who was Osama bin Laden's mentor .... [Azzam] had established the Al Kifah Refugee Center [Brooklyn, New York] to function as its worldwide recruiting post, propaganda office, and fund-raising center for the mujahideen fighting in Afghanistan ...

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)[43][44] 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.

[45] 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.

[82] 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.

In his testimony, Majid Khan stated that he provided Siddiqui with money, photos, and a completed application for an "asylum travel form" that "looked and functioned like a passport".

[82] 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.

[17] The file included evidence from Khalid Sheikh Muhammad (KSM), the al-Qaeda chief planner of the 11 September 2001 attacks, who was interrogated and tortured (waterboarded 183 times)[88] after his arrest on 1 March 2003.

[91] 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.

[98] 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.

[19] 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.

[61][48] 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.

[103] Investigating the disappearance, 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.

[107][108] According to journalist, Muslim convert, and former Taliban captive Yvonne Ridley, Siddiqui spent those years in solitary confinement at Bagram as "Prisoner 650".

[15][120] According to Rolf Mowatt-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 ...

"[15][122] 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.

[1][51] 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, as well as the mortality rates of certain weapons and handwritten notes referring to a "mass casualty attack" that listed various US 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.

[31] 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 US 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.

[71][67][91][134] 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.

[137] FBI reports maintained that Siddiqui told a US 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.

"[149] On 4 August 2008, Siddiqui was placed on an FBI jet and flown to New York City[48] after the Afghan government granted extradition to the United States for trial.

[31] 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.

[174] 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.

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.

[188] She was visited by her sister Fowzia Siddiqui in May 2023, accompanied by human rights lawyer Clive Stafford Smith and Jamaat-e-Islami senator Mushtaq Ahmad Khan.

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.

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.

[19]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.

On 2 November, Attorney General of Pakistan Mansoor Usman Awan informed the Islamabad High Court that a Pakistani delegation is scheduled to visit the United States following the presidential elections to negotiate the release of Siddiqui.