Updated

A Colorado shuttle driver from Afghanistan reportedly amassed bomb-making ingredients by traveling from one beauty supply store to another, buying large amounts of hydrogen peroxide and nail polish remover, the Justice Department said Thursday.

Najibullah Zazi, 24, plotted for more than a year to set off bombs in the United States — specifically on New York City trains and subways, according to federal documents.

Zazi was indicted Thursday on federal charges of conspiracy to use weapons of mass destruction in a possible Al Qaeda-linked bomb plot on United States soil.

If the allegations prove true, this could be the first operating Al Qaeda cell to be uncovered inside the U.S. since the Sept. 11, 2001, attacks.

A police source told The Associated Press that Zazi may have bought some of the bomb-making supplies using associates who paid for them with stolen credit cards.

A senior official familiar with the investigation said associates of Zazi visited Colorado from New York to help him buy the chemicals. The official said they used stolen credit cards to make the purchases and then returned to New York.

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Authorities believe that Zazi and others may have been planning a mass transit attack in New York City similar to those on subways in London and Madrid.

"We are investigating a wide range of leads related to this alleged conspiracy, and we will continue to work around the clock to ensure that anyone involved is brought to justice," Attorney General Eric Holder said in a statement. "We believe any imminent threat arising from this case has been disrupted."

The government says he planned to use explosives "against persons or property in the United States."

Zazi. an Afghanistan native who is a legal permanent resident of Aurora, Colo., was previously charged with the lesser offense of lying to the government for his suspected involvement in the New York-Denver-based scheme.

Two others, Zazi's father Mohammed Zazi and controversial Queens, N.Y., imam Ahmad Wais Afzali, also are charged with lying to federal agents from the FBI trying to uncover the plot.

Authorities hadn't determined a time and place of a possible attack.

The two-page indictment offers few details, but a separate document — a government motion seeking to deny Zazi's bail — lays out evidence gathered by investigators.

The Denver airport shuttle driver began plotting to "use one or more weapons of mass destruction" between Aug. 1, 2008, and September 2009 against the United States, the papers say.

The document says that on Sept. 6 and 7, Zazi tried to communicate with another person "seeking to correct mixtures of ingredients to make explosives."

"Each communication," the papers say, was "more urgent than the last."

On those days, Zazi rented a suite at a hotel in Aurora, authorities charge. The room had a kitchen, and subsequent FBI testing for explosives and residue in the suite found the presence of residue in the vent above the stove.

In July and August, Zazi bought unusually large amounts of hydrogen peroxide and acetone — a solvent commonly found in nail polish remover — from beauty supply stores in the Denver metropolitan area, the document says.

He searched the Internet for home improvement stores in Queens before driving a rental car for a two-day trip to the city, the document said.

Zazi has publicly denied any terrorism plotting.

A series of searches in Denver and New York City over the past two weeks — including high-profile raids on Queens apartments that netted backpacks, cell phones and a scale — haven't found any evidence of explosives.

Beauty supply store employees in New York and the Denver suburbs said authorities had been there recently asking whether large quantities of hydrogen peroxide or acetone supplies had been purchased.

Zazi, his 53-year-old father and Afzali, 37, were arrested over the weekend. They were in federal court in Denver and New York Thursday morning.

On Thursday, Zazi's father was freed on $50,000 bail after detention hearings and Afzali was released on $1.5 million bond. The two will be closely monitored with ankle bracelets. Zazi remained detained Thursday. The government is fighting to have his bail denied.

Authorities say they found bomb-making instructions on a hard drive on Zazi's laptop computer but still were unsure of the specific target or scope of a possible terrorist attack. They say they have linked Zazi to Al Qaeda.

The Justice Department accused the Denver airport shuttle driver of "knowingly and intentionally" plotting with others "to use one or more weapons of mass destruction, specifically explosive bombs and other similar explosive devices."

The indictment also alleges that Zazi and others traveled within the United States and overseas and used e-mail and the Internet in plotting the bombings.

Also Thursday, reports emerged of a 1992 guilty plea by Afzali to sexual assault charges. FOX News has not confirmed those reports.

On Wednesday, hundreds of federal agents and New York investigators again fanned out in the Queens neighborhood where apartments were searched last week to re-interview "people previously encountered" during the earlier raids.

Phone and other records were being reviewed that could link potential suspects to each other or locate new ones.

"Many of the people we've spoken to have been cooperative," an official told The Associated Press on condition of anonymity.

Questions lingered about whether early missteps hindered the investigation. A criminal complaint suggests police acting without the FBI's knowledge might have inadvertently blown the surveillance and forced investigators' hand by questioning Afzali — considered a trusted police source in the community — about Zazi and other possible plotters.

The imam, it says, turned around and tipped off Zazi by calling him the next day and saying in a recorded conversation, "They asked me about you guys."

In a joint statement, Police Commissioner Raymond Kelly and Joe Demarest, head of the FBI office in New York, denied reports that the questioning of Afzali and his alleged betrayal had caused a rift between the agencies.

The New York Times, quoting unnamed current and former police officials, reported in Thursday editions that the New York Police Department transferred two commanders this week, including one from its counterterrorism bureau. NYPD top spokesman Paul Browne would not confirm the transfers or comment late Wednesday.

FOX News' Catherine Donaldson-Evans, Alicia Acuna, David Lee Miller and The Associated Press contributed to this report.