ISLAMABAD: Aafia Siddiqui, the Pakistani neuroscientist whose case has become a flashpoint of Pakistani-American tensions, plotted to smuggle explosives into America and offered to manufacture biological weapons, according to the Guantanamo files.

The allegations are a combination of US intelligence analysis and direct testimony by at least three senior Al Qaeda figures, including the 9/11 plotter Khalid Sheikh Muhammad. They cannot be independently corroborated and the testimonies were likely to have been extracted under conditions of torture. Muhammad, known as KSM in intelligence circles, was waterboarded 183 times in the month after his capture in Pakistan in March 2003.

But several of the accounts do overlap, linking Siddiqui, a 39-year-old mother of three, with some of Osama bin Laden's top lieutenants. They help explain why the FBI placed her on a list of the world's seven most wanted Al Qaeda fugitives in 2004.

Siddiqui disappeared from Karachi in March 2003 only to reappear five years later in murky circumstances in Ghazni, Afghanistan. There was an altercation in a police station and the US accused Siddiqui of trying to shoot two soldiers and two FBI agents. She was sent to the US, tried, and last year sentenced to 86 years in jail. In Pakistan she became a cause celebre.

The Guantanamo files offer a murky perspective, placing Siddiqui at the heart of an Al Qaeda cell based in Karachi between 2002 and 2003. Led by KSM, the cell conspired to mount fresh attacks in the US, on London Heathrow airport and inside Pakistan.

According to the files, the cell planned to smuggle explosives into America under the cover of textile exports and attack “economic targets”, according to KSM.

The operation would take place through an import-export business run by Saifullah Paracha, a Pakistani businessman who worked as a New York travel agent for 13 years before developing ties to Osama bin Laden. Paracha, 64, is currently in Guantanamo Bay.

According to Paracha's file, Siddiqui's role was to “rent houses and provide administrative support for the operation”. As part of this brief she travelled from Pakistan to the US in January 2003 to help renew the American travel papers of Majid Khan, a co-conspirator.

According to Khan, he provided Siddiqui with money, photos and a completed application for an “asylum travel form” that “looked and functioned like a passport”.

Then, according to Khan's file, “Siddiqui returned to the US and opened a post office box in detainee's name, using her driver's licence information”.

The plot collapsed after Khan was picked up in Pakistan and sent to Guantanamo. A co-conspirator in America, Uzair Paracha, son of Saifullah Paracha, was arrested in possession of the post box key. Uzair was sentenced to 30 years’ jail in 2006; details of Siddiqui's role surfaced during his trial. Her family say she was framed.

The Guantanamo files give fresh details on Siddiqui's relationship with Ammar Baluchi, the nephew of KSM and a senior Al Qaeda figure facing a raft of serious allegations. Siddiqui reportedly married Baluchi during a secret ceremony near Karachi in February 2003. Siddiqui's family denies the marriage took place.

Baluchi said he told Siddiqui, who has a biology degree from MIT, that Al Qaeda had set up a laboratory to make biological weapons. Siddiqui replied that she “was willing to participate in a biological weapons project if Al Qaeda tasked her to”. Al Qaeda has a biological weapons programme based in Afghanistan stretching back to the late 1990s. When Siddiqui was arrested in Ghazni in 2008, her handbag allegedly contained several bottles of deadly chemicals, extracts from an “arsonist's handbook”, and details of several prominent American landmarks.

Despite the serious nature of the allegations against Siddiqui contained in the Guantanamo files, the US has never attempted to prosecute her for them. In last year's court case she was charged with attempted murder.—Dawn/Guardian News Service