A federal prosecutor argued that Najibullah Zazi of Denver was planning an attack to coincide with the 9/11 anniversary.
"The evidence suggests a chilling, disturbing sequence of events showing the defendant was intent on making a bomb and being in New York on 9/11, for purposes of perhaps using such items," prosecutor Tim Neff told U.S. Magistrate Judge Craig Shaffer.
Zazi is charged with conspiring to use weapons of mass destruction in a plot authorities say was aimed at commuter trains.
His attorney said that claims the Afghan immigrant was on the verge of unleashing a terrorist attack on New York City are missing a key element: explosives or the chemicals allegedly used to make them.
FBI agents have yet to find those elements and connect them to Zazi, attorney Arthur Folsom told a federal judge in Denver Friday.
"No traces of any kind of chemical was found in his vehicle," Folsom said of an FBI search of Zazi's car.
Shaffer ultimately ordered Zazi's transfer to New York, and Zazi was taken there by federal marshals.
Read more about Zazi's indictment
Zazi was stopped by police on Sept. 10 as he entered New York, and he dropped his plans for an attack once he realized that law enforcement was on to him, prosecutors allege.
Prosecutors said Zazi received explosives training from al Qaeda in Pakistan and returned to the U.S. bent on building a bomb.
CBS News correspondent Bob Orr reports that surveillance videotapes and receipts from a Denver area beauty supply shop show terror suspect Najibullah Zazi twice bought large amounts of hydrogen peroxide - a key ingredient in the kind of homemade explosives that, sources claim, Zazi hoped to unleash on New York.
"When the FBI asked if we had anybody purchasing large volumes, all we had to do was go through our transaction history and those two popped up," Karan Hoss of Beauty Supply Warehouse told CBS News.
At least three and possibly more of his accomplices remain at large, and investigators have fanned out across New York in pursuit of suspects. Authorities also issued a flurry of terrorism warnings for sports complexes, hotels and transit systems.
A law enforcement official who spoke on condition of anonymity because of the ongoing investigation said associates of Zazi visited Colorado to help him buy the chemicals using stolen credit cards before returning to New York.
Another law enforcement official said that authorities had been especially worried about Zazi's Sept. 10 visit to the city because it coincided with a visit by President Barack Obama. Police considered arresting him right away. The official spoke on condition of anonymity because the investigation continues.
Police have been especially active in the neighborhood in Queens where Zazi visited during his New York trip, staying at an apartment with a group of cab drivers and food cart operators he knows.
Zazi's attorney Folsom said prosecutors lack direct evidence that Zazi was involved in bomb-making, finding none of those materials in Zazi's car, his Aurora, Colo., apartment or apartments Zazi visited in New York. FBI agents said they found Zazi's fingerprints on a scale and batteries during a search in Queens, but Folsom said those items have no connection to the alleged plot.
"I think they were hoping that people would just jump to conclusions," Folsom said in an interview with The Associated Press.
Zazi ran a coffee cart in Manhattan before moving to Denver this year and getting a job as an airport shuttle driver.
FBI raids beginning Sept. 14 rattled a quiet, predominantly Asian neighborhood in Queens. Muslim men said dozens of FBI agents ransacked their homes and questioned them for hours, sometimes taking DNA samples and prints from their shoes.
The FBI has also been visiting beauty shops and home-improvement stores in Colorado and New York for details about the alleged bomb-making purchases.
Court papers say that during the summer, Zazi and three unidentified associates bought "unusually large quantities" of hydrogen peroxide and acetone - a flammable solvent found in nail-polish remover - from Denver-area beauty supply stores. The products had names such as Ion Sensitive Scalp Developer and Ms. K Liquid 40 Volume.
Zazi also searched the Web site of a Queens home-improvement store for another ingredient needed to make a compound called TATP (triacetone triperoxide), the explosives used by shoe bomber Richard Reid and the terrorists who carried out the London bombings that killed more than 50 people, according to court papers.
Zazi intensified his bomb-making experiments this month, cooking up substances in a Colorado hotel suite he rented on Sept. 6-7 before driving 1,600 miles to New York over the course of about two days. He became aware that law enforcement was onto him when he was stopped entering the city on Sept. 10, causing the plot to unravel.
Neff said Zazi "was in the throes of making a bomb and attempting to perfect his formulation" and seeking information on how to use flour to make the explosive suitable for transporting.
"He was asking for information on flour and how to get the contents right," Neff said in court.
The Metropolitan Transportation Authority - which runs New York City's subway system, buses and commuter rails - declined to comment on the revelation of a Sept. 11-timed plot. It reissued a statement from earlier in the week that it has boosted its police presence at "key commuter rail locations" since the terror threat became public.
Federal agents and police officers in New York visited up to 200 locations a day in the area during the probe, including beauty-supply stores, extended-stay hotels that have rooms with kitchens, hardware stores, truck rental agencies and storage facilities.
Zazi was scheduled to appear in federal court Tuesday in Brooklyn.
A government request to deny bail laid out a chronology of the alleged scheme, which prosecutors said had been in the works for more than a year.
On Sept. 6 and 7, Zazi checked into a suite at a Colorado hotel with a kitchen and a stove, government papers say, and tried to contact an unidentified associate "seeking to correct mixtures of ingredients to make explosives."
"Zazi repeatedly emphasized in the communications that he needed the answers right away," the papers said, adding that each communication was "more urgent than the last."
Beauty supply store employees in New York and the Denver suburbs said authorities had been asking whether anyone had come in buying a lot of hydrogen peroxide or acetone.
While FBI agents continue to press Zazi's associates and search for possible hidden explosives, - charged in separate schemes unrelated to Zazi's alleged plot.
Nineteen-year old Hosam Smadi is accused of attempting to blow up a Dallas high-rise; and Michael Finton is charged with trying to bomb the federal courthouse in Springfield, Illinois.
Both men were caught in FBI stings this week, with undercover agents acting as fellow terrorists and providing dummy bombs. Officials say that, unlike Zazi, the men presented no real danger.
But they underscore the ongoing threat from homegrown radicals.
"There are people living in the United States who may be U.S. citizens or legal residents who want to carry out violent acts, said CBS News national security analyst Paul Kurtz.