Zazi and two other defendants have not been charged with any terrorism counts, only the relatively minor offense of lying to the government. But the case could grow to include more serious charges as the investigation proceeds.
Zazi has publicly denied being involved in a terror plot, and defense lawyer Arthur Folsom dismissed as "rumor" any notion that his client played a crucial role.
Publicly, law enforcement officials have repeatedly said they are unaware of a specific time or target for any attacks.
Privately, officials speaking on condition of anonymity because they were not authorized to discuss the case said investigators have worried most about the possible use of backpack bombs on New York City trains, similar to attacks carried out in London and Madrid.
The investigation into Zazi's role and how many others may be involved was ongoing. Two law enforcement officials speaking on condition of anonymity because they were not authorized to discuss details of the investigation told The Associated Press late Monday that more than a half-dozen individuals were being scrutinized in the alleged plot.
The FBI said in a statement that "several individuals in the United States, Pakistan and elsewhere" were being investigated.
Backpacks and cell phones were seized last week from apartments in Queens where Zazi visited.
In a bulletin issued Friday, the FBI and Homeland Security Department warned that improvised explosive devices are the most common tactic to blow up railroads and other mass transit systems overseas. And they noted incidents in which bombs were made with peroxide.
In the bulletin, obtained by The Associated Press, officials recommended that transit systems conduct random sweeps at terminals and stations and that law enforcement make random patrols and board some trains and buses.
The effects of the warning were not immediately clear Monday. New York's transit agency said it was in touch with an FBI-NYPD task force but wouldn't comment further.
The task force feared Zazi may have been involved in a potential plot involving hydrogen peroxide-based explosives, according to two law enforcement officials, who spoke on condition of anonymity because they were not authorized to discuss the investigation.
Investigators said they found notes on bomb-making instructions that appear to match Zazi's handwriting, and discovered his fingerprints on materials - batteries and a scale - that could be used to make explosives. He also made a trip to Pakistan last year in which he received al-Qaida explosives and weapons training, the government said.
Zazi, a legal resident of the U.S. who immigrated in 1999, told the FBI that he must have unintentionally downloaded the notes on bomb-making as part of a religious book and that he deleted the book "after realizing that its contents discussed jihad."
A strange sequence of events began to unfold nearly two weeks ago when Zazi - already under surveillance by federal agents - rented a car in Colorado and made a 1,600-mile trek across the heartland to New York. He told reporters that he went to New York to resolve an issue with a coffee cart he owned.
He was briefly stopped entering the city as part of what was believed to be a routine drug check, and proceeded to his friend's place in Queens. Once there, his car was towed and authorities confiscated his computer. He was told by an NYPD informant that detectives were asking about him, and decided to cut the trip short and fly back to Colorado, authorities said.
Their surveillance blown and their main suspect flying back to Colorado, officials speeded up the investigation and launched raids on several Queens apartments in a search for evidence of explosives.
"Whatever investigative interest this guy held prior to that time, when it became clear he was leaving for New York shortly before Sept. 11, my guess is he became a much brighter blip on their radar screen," said Pat Rowan, the former head of the Justice Department's National Security Division.
Since 2001, counterterrorism officials have shifted their approach and made the disruption of plots in their early stages a top priority, ahead of amassing incriminating evidence of more serious crimes. The exceptions to the rule are plots infiltrated by informants who are being directed by the FBI every step of the way.
"In the current environment when plotters are disrupted before their plot becomes concrete, you may end up with something that looks relatively trivial to the legal system, but the truth is you can't judge their efforts by the legal charges they're able to bring," Rowan said.
Zazi and his 53-year-old father, Mohammed Wali Zazi, were arrested Saturday in Denver. Ahmad Wais Afzali, 37, was arrested in New York, where he is an imam at a mosque in Queens. The three are accused of making false statements to the government. If convicted, they face eight years in prison.
On Monday, Najibullah Zazi answered the judge's questions politely with a "Yes, honor" or "No, honor."
Afzali, with a long dark beard and wearing a tunic, was ordered held without bail after prosecutors said they believed he might flee if released. He smiled and blew kisses to his wife and other relatives before deputy marshals led him out of the courtroom.
His attorney, Ron Kuby, accused authorities of trying to make Afzali a scapegoat for a botched investigation. Kuby told reporters outside court that before Afzali's arrest, authorities had begged him to help them in the Zazi investigation. He said his client knew he was being recorded, and never tried to mislead the FBI.
"They blew their own investigation and now they're trying to blame my client," he said.
Zazi's father could be released Thursday and placed under electronic monitoring at home and have his passport confiscated.
Mohammed Zazi and Afzali are accused of lying to FBI agents about calls between Denver and New York. Investigators said Afzali lied about a call in which he told Najibullah Zazi that he had spoken with authorities.
Zazi's father is accused of lying when he told authorities he didn't know anyone by the name of Afzali. The FBI said it recorded a conversation between Mohammed Zazi and Afzali.
Bill Taylor, a former U.S. prosecutor in Denver, said Afzali may have forced the FBI's hand to act as quickly as it did.
"They don't want to move in until they can identify everyone they think is involved," Taylor said. "In this case it wasn't possible. So the second best option is to gather what you can, get placeholder charges that may or may not last for a lawful detention, then proceed to possible bigger charges such as conspiracy or giving material aid to terrorism."
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