Prosecutors claim Najibullah Zazi, the 24-year-old Afghan immigrant who received training in Pakistan, was planning to strike another New York City target on 9/11, this time with homemade bombs.
The CIA learned about Zazi through one of its sources and alerted domestic agencies, including the FBI, intelligence officials said.
U.S. intelligence organizations first became aware of Zazi in late August, a senior administration official said. The intelligence and administration officials declined to offer more details on the operative and spoke on condition of anonymity because the investigation is ongoing.
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The fact that intelligence officials learned of Zazi through a CIA source sheds more light on the government's claim that the charges against him are part of a broader, international case and begins to explain why the investigation triggered such a large offensive from the nation's intelligence community.
It also shows the case stems from the CIA's counterterrorism efforts to track al Qaeda rather than an investigation initiated in this country by someone's suspicious actions, like most other domestic terrorism cases handled by the FBI.
President Barack Obama began receiving briefings on the investigation in late August, updated at least daily and sometimes several times a day as intelligence officials were crafting their case against Zazi, senior administration officials said.
Zazi initially was characterized to Obama as a person of interest because of suspected involvement in terrorist activities, the officials said. Obama's primary interest in those briefings was to ensure an attack was prevented and all involved in the plot were identified, the officials said.
The CIA declined to comment Monday, spokesman George Little said.
Federal agents began watching Zazi in Denver in early September. He drove a rental car to New York on Sept. 9, but left the city to return to Denver on Sept. 12 after learning that investigators were looking for him, prosecutors said. FBI agents raided three apartments in Queens two days after Zazi left the New York area.
Zazi and his lawyer agreed to meet with investigators at FBI offices in Denver on Sept. 16. After three days of meetings, Zazi was arrested and charged with lying to federal agents.
Speaking Monday in Colorado at a conference of police chiefs, Attorney General Eric Holder said the plot had the potential to kill scores of people.
Zazi is the only suspect publicly identified in the terror plot. More arrests are expected. Prosecutors have said three others in New York City worked with Zazi, although they do not currently pose a threat.
Calls to Zazi's lawyer were not returned Monday.
Zazi was initially arrested on charges that he lied to federal investigators. He remains held without bond and has pleaded not guilty to conspiring to use weapons of mass destruction. The charges related to his statements to investigators later were dropped.
Zazi's father, Mohammed Wali Zazi, and a Queens, N.Y., imam, Ahmad Wais Afzali, face charges of lying to investigators last month when first questioned about Zazi.
Prosecutors said Zazi received explosives training at an al Qaeda training camp. They have accused him of planning an attack in New York, perhaps on the city's subway system around the anniversary of the 9/11 World Trade Center attack, using powerful homemade bombs of hydrogen peroxide and flour. Would-be shoe bomber Richard Reid attempted to use the same type of explosive in 2001 to destroy an airliner, and the material was used by the terrorists in the London bombings in 2005 that killed 52 people.
Zazi was recruited and trained by al Qaeda to make the bombs from common supplies purchased at beauty supply stores, intelligence officials said, although they declined to say when that occurred. Zazi's contact with the senior al Qaeda operative occurred through an intermediary, one official said.
Zazi, who moved to the U.S. with his family as a teenager, has denied any involvement in a terror plot. He has said his travels to Pakistan, which began in 2006, were to visit family, including his wife, whom he married on that first trip.
The case against Zazi involves classified information as well as evidence, collected by the FBI in searches of Zazi's computer, that discussed bomb making.
Prosecutors submitted court documents saying they intend to use electronic information the FBI obtained through the use of the Foreign Intelligence Surveillance Act.