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In the summer of 2008, a shopkeeper in the Afghan city of Ghazni noticed a strange sight: a woman in burqa drawing a map. In a region where nearly all females are illiterate, he found it suspicious and called the police, according to an Afghan intelligence official.

In her bag, police found two pounds of deadly poison, as well as hundreds of handwritten notes on making not only bombs and viruses, but machines to bring down US drones, according to US court documents.

The woman turned out to be a Pakistani named Aafia Siddiqui ’95, an MIT-and Brandeis-trained scientist who spent years in Boston before returning to Pakistan and vanishing with her three children in 2003.

Siddiqui, 37, standing trial beginning yesterday in a federal courtroom in New York, accused of grabbing a rifle and trying to shoot the FBI agents who came to interview her in Ghazni. If convicted, she faces life in prison.

The testimony will hinge on narrow questions of her actions when she was confronted by US agents, but the trial may also help settle a lingering mystery that hangs over her strange story: Where was Siddiqui from 2003 until her capture in 2008?

After her disappearance, Siddiqui’s family said she was abducted and tortured by US intelligence agents. She has become a cause celebre in Pakistan, as thousands routinely rally in her support, chanting anti-American slogans with posters of her photograph. The government of Pakistan is paying for her defense.

But US officials insist that Siddiqui ran away to join a militant group, and prosecutors have filed documents that portray her as an anti-American fighter in Pakistan’s lawless border areas during her years of absence.

“The US government had an interest in clearing up … what they say are wild charges,” said Tom Malinowski, Washington advocacy director for Human Rights Watch, one of several groups that included Siddiqui’s name in reports about possible secret CIA prisoners but never drew a final conclusion as to what happened to her. “It matters where she has been for the last five years. I don’t know what the truth is.”

Pretrial documents filed by prosecutors allege that Siddiqui, who graduated from MIT in 1995 with a biology degree, was a fervent believer in jihad and interested in weaponry. Some of her behavior and statements were seemingly bizarre, leading to a court-ordered evaluation of her mental status, which has also been in dispute.

One document filed by the government, written in Siddiqui’s own handwriting, says: “It is better to die while fighting infidels than to die or become handicapped by one’s own negligence and carelessness when making weapons.”

Other documents in her possession at the time of her capture explained the manufacture of C-4 explosives, gun power, and deadly germs, although some papers described weapons that would be almost impossible to make, such as viruses that do not attack children.

Siddiqui’s lawyers have maintained that she was abducted, by either the United States or Al Qaeda, and that as a result is suffering from a mental illness caused by post-traumatic stress.