Accused Al Qaeda sleeper agent held

One of the more elusive and mysterious figures linked to Al Qaeda -- a Pakistani mother of three who studied biology at MIT and who authorities say spent years in the United States as a sleeper agent -- was flown to New York on Monday night to face charges of attempting to kill U.S. military and FBI personnel in Afghanistan.

The Justice Department, FBI and U.S. military in Afghanistan said that Aafia Siddiqui, 36, was arrested in Ghazni province three weeks ago. She is accused of firing an automatic rifle at FBI agents and soldiers and is scheduled to appear before a federal judge in Manhattan today.

Authorities believe Siddiqui used the technical skills she acquired at the Massachusetts Institute of Technology to do what virtually no other woman has accomplished -- work her way into the clubby inner circles of Al Qaeda’s command and control operation, including its chemical and biological weapons program.

But questions swirled around her Monday evening, including whether she has been in Pakistani custody for at least part of the last five years and whether there is hard evidence that she was a trained, committed and hardened Al Qaeda operative, as former Atty. Gen. John Ashcroft and other U.S. officials have contended.

“This doesn’t pass the sniff test,” Elaine W. Sharp, a Massachusetts defense lawyer representing Siddiqui, said of the circumstances surrounding her client’s arrest. She said her client was not an Al Qaeda terrorist, but an innocent woman who had been held at Bagram air base in Afghanistan or elsewhere for the last several years and tortured by some combination of U.S., Pakistani and Afghan officials.

Sharp said that Siddiqui had obtained an undergraduate biology degree from MIT and a doctorate in behavioral neuroscience from Brandeis University, both near Boston, and that she had lived a quiet life in the Boston area, and in Houston before that, before returning to her native Pakistan in late 2002.

One senior U.S. federal law enforcement official refused to comment on the case, except to say that Siddiqui was an extremely significant catch and that authorities had pledged not to discuss any details of the operation because of its sensitivity and relationship to ongoing counter-terrorism operations.

“We can’t say anything about this one,” said the official, who spoke on the condition of anonymity. He confirmed that the woman in custody was the one near the top of the FBI’s Most Wanted List of fugitive terrorism suspects wanted for questioning.

For years, the FBI and the CIA have been desperately trying to find Siddiqui, who they say spent several years in Boston as a “fixer” for admitted Sept. 11 mastermind Khalid Shaikh Mohammed, providing haven and logistical support for terrorist operatives that he sent to the United States to launch attacks.

Siddiqui also bought diamonds in Liberia as part of Al Qaeda financing efforts and married Mohammed’s nephew, Ali Abdul Aziz Ali, according to several U.S. counter-terrorism officials and government documents.

One former CIA weapons of mass destruction analyst who tracked Siddiqui said that she became extremely frustrated years ago, however, when she was told by senior Al Qaeda leaders to help their cause by getting pregnant.

“They told her that the best thing she could do for Al Qaeda was to start popping out little jihadists,” said the former CIA officer, who left the agency in 2006. “She was furious; she knows more about this stuff than pretty much anyone in the organization.”

Siddiqui never gave up her desire to launch attacks against the United States and its allies, according to FBI and Justice Department records made public Monday night.

According to court papers, Afghan national police officers in Ghazni province, south of Kabul, the capital, observed Siddiqui acting suspiciously near the provincial governor’s compound July 17.

When they searched her handbag, they found documents relating to explosives, chemical weapons and weapons involving biological materials and radiological agents, along with descriptions of landmarks in New York City and elsewhere in the United States, and liquid and gel substances sealed in bottles and jars.

The next day, according to the court papers, she was being questioned by two FBI agents, an Army captain and an Army warrant officer, along with their interpreters.

“In the area where she was sequestered, they put their weapons down while trying to talk to her, and she seized a weapon and began to shoot,” Lt. Col. Rumi Nielson-Green, a spokeswoman for U.S. forces at Bagram air base, said today. “Our officer returned fire. She was shot in the stomach, but continued to struggle.”

She was subsequently hospitalized at Bagram and “was not in the detention facility at any time,” Nielson-Green said. Siddiqui was flown to the United States after being found well enough to travel, the spokeswoman said.

Siddiqui is charged in a criminal complaint filed in the Southern District of New York with one count of attempting to kill United States officers and employees and one count of assaulting U.S. officers and employees. If convicted, she faces a maximum sentence of 20 years in prison on each charge.

Michael J. Garcia, the U.S. attorney in New York, praised the investigative work and said the investigation was continuing.

In the past Siddiqui’s lawyer, some human rights advocates and Siddiqui’s family members have said she disappeared with her three children in March 2003 while visiting her parents’ home in Karachi -- around the same time the FBI said it wanted to question her. Mohammed was arrested just before that in Pakistan.

In 2006, Amnesty International listed Siddiqui as one of many “disappeared” suspects in the U.S.-led war on terrorism. Of allegations that Siddiqui had been detained at Bagram after her disappearance in Pakistan, Nielson-Green said: “That’s absolute nonsense.”

Pakistani government spokesmen declined to comment on the case early today.

Sharp said that the U.S. government’s accusations were untrue, that Siddiqui’s three children have never surfaced and that her family believes that public pressure from Amnesty and other organizations prompted authorities to concoct her suspicious behavior and arrest so they could hide the fact that she has been in custody all this time.

“We thought she was dead until her brother in Houston got a visit from the FBI the other day and said she is alive,” Sharp said.

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josh.meyer@latimes.com

Times staff writer Laura King in Kabul contributed to this report.