WASHINGTON — An American-trained Pakistani neuroscientist with ties to operatives of Al Qaeda has been charged with trying to kill American soldiers and F.B.I. agents in a police station in Afghanistan last month, the Justice Department said Monday night.
The scientist, Aafia Siddiqui, who studied at Brandeis University and the Massachusetts Institute of Technology, was transferred to New York on Monday, and is to be arraigned Tuesday in the United States District Court for the Southern District of New York, the department said in a statement.
Ms. Siddiqui, 36, disappeared with her three children while visiting her parents’ home in Karachi, Pakistan, in March 2003, leading human rights groups and her family to believe she had been secretly detained. But in interviews Monday and in a criminal complaint made public later Monday, American officials said they had no knowledge of Ms. Siddiqui’s location for the past five years until July 17, when Ms. Siddiqui and a teenage boy were detained in Ghazni, Afghanistan, after local authorities became suspicious of their loitering outside the provincial governor’s compound.
When they searched Ms. Siddiqui’s handbag, the Afghan police found documents describing the creation of explosives as well as excerpts from the “Anarchist’s Arsenal.” She also carried sealed bottles and glass jars filled with liquids and gels.
The day after she was detained, an American team, including two F.B.I. agents, two American soldiers and interpreters, went to the police station to talk to her. The F.B.I. has wanted her for questioning since May 2004, a Justice Department spokesman said.
The complaint gave the following account of what happened next. Americans entered a room in the police station, unaware that Ms. Siddiqui was being held there, unsecured, behind a curtain. One of the soldiers, a warrant officer, sat down and placed his M-4 rifle on the floor next to the curtain.
Shortly after the meeting began, the other soldier, a captain, heard a woman yelling from the curtain. He turned to see Ms. Siddiqui pointing the warrant officer’s rifle at him.
The interpreter sitting closest to Ms. Siddiqui lunged at her and pushed the rifle away as she pulled the trigger and shouted, “God is Great.” She fired at least two shots, but no one was hit. The warrant officer returned fire with his 9mm pistol, hitting Ms. Siddiqui at least once in the torso.
Ms. Siddiqui struggled when officers tried to subdue her, shouting in English that she wanted to kill Americans. After she was subdued, the complaint said, she “temporarily lost consciousness.”
Ms. Siddiqui was charged Monday with one count of trying to kill American officers and employees and one count of assaulting them, the Justice Department said. If convicted, she faces a maximum sentence of 20 years in prison for each count.
The wild scene in the police station is the latest chapter in one of the strangest episodes in the American campaign against terrorism.
Human rights groups and a lawyer for Ms. Siddiqui, Elaine Whitfield Sharp, said they believed that Ms. Siddiqui had been secretly detained since 2003, much of the time at Bagram Air Base in Afghanistan.
“We believe Aafia has been in custody ever since she disappeared,” Ms. Sharp said in an interview on Monday before the complaint was made public, “and we’re not willing to believe that the discovery of Aafia in Afghanistan is coincidence.”
But American military and intelligence officials said Ms. Siddiqui was in Pakistan until she was detained by Afghan authorities.
“She was not in U.S. custody,” said a senior American intelligence official, who spoke on condition of anonymity because of the pending legal action.
United States intelligence agencies have said that Ms. Siddiqui has links to at least 2 of the 14 men suspected of being high-level members of Al Qaeda who were moved to Guantánamo in September 2006.
A government statement said that Ms. Siddiqui helped Majid Khan, a former Baltimore resident and terrorism suspect held in Guantánamo, get documents to re-enter the United States. The statement said Mr. Khan was directed by Khalid Shaikh Mohammed, the chief organizer of the Sept. 11 attacks, to conduct research on poisoning reservoirs and blowing up gas stations in the United States. The statement also said he had delivered money for terrorist attacks to another operative and discussed a plan to smuggle explosives.
The government said that Ali Abd al-Aziz Ali, known as Ammar al-Baluchi, a nephew of Mr. Mohammed’s, ordered Ms. Siddiqui to help get Mr. Khan’s paperwork. The statement said Mr. Baluchi and Ms. Siddiqui married shortly before his capture.