Khan's explanation is bolstered by the one person who claims to have met the missing neuroscientist between 2003 and 2008 – her uncle, Shams ul-Hassan Faruqi. Back in Islamabad, I went to see him.
A sprightly old geologist, Faruqi works from a cramped office filled with coloured rocks and dusty computers. Over tea and biscuits he described a strange encounter with his niece in January 2008, six months before she was captured in Afghanistan.
It started, he said, when a white car carrying a burka-clad woman pulled up outside his gate. Beckoning him to approach, he recognised her by her voice. "Uncle, I am Aafia," he recalled her saying. But she refused to leave the car and insisted they move to the nearby Taj Mahal restaurant to talk. Amid whispers, her story tumbled out.
Siddiqui told him she had been in both Pakistani and American captivity since 2003, but was vague on the details. "I was in the cells but I don't know in which country, or which city. They kept shifting me," she said. Now she had been set free but remained under the thumb of intelligence officials based in Lahore. They had given her a mission: to infiltrate al-Qaida in Pakistan. But, Siddiqui told her uncle, she was afraid and wanted out. She begged him to smuggle her into Afghanistan into the hands of the Taliban. "That was her main point," he recalled. "She said: 'I will be safe with the Taliban.'"
That night, Siddiqui slept at a nearby guesthouse, and stayed with her uncle the next day. But she refused to remove her burka. Faruqi said he caught a glimpse of her just once, while eating, and thought her nose had been altered. "I asked her, 'Who did plastic surgery on your face?' She said, 'nobody'."