The emerging details show that Najibullah Zazi, who has admitted receiving weapons training from al Qaeda, played a direct role in an alleged terror plot, authorities said court documents released Sunday.
"I think this demonstrates despite what some have said that the safe haven in Pakistan and al Qaeda core still matter; they still matter because there is training underway," said CBS News national security analyst Juan Zarate. "There are westerners, including people from the U.S., who are willing to travel there to connect to al Qaeda to be launched and sent back."
Zazi, 24, has publicly denied being involved in terror plot. Zazi, his father, and an Imam in New York City were arrested late Saturday on charges of making a false statement to the government, though legal experts say more charges could be coming.
Also arrested Sunday were Zazi's father, Mohammed Wali Zazi, 53, in Denver; and an associate, Ahmad Wais Afzali, 37, of New York City, the Justice Department said Sunday. Both also were charged with making false statements to federal agents, which carries a penalty of eight years in prison.
Zazi's defense team denied reports that Zazi considered a plea deal related to terror charges, and Zazi's attorney, Arthur Folsom, dismissed as "rumor" any notion that Zazi played a crucial role. Zazi's defense team did not respond to repeated attempts to reach them Sunday.
Federal officials in Denver declined to comment.
The FBI is investigating several individuals in the United States, Pakistan and elsewhere in an alleged plot to detonate explosive devices in the United States, the Justice Department said.
Zazi admitted to FBI agents that he received instructions from al Qaeda operatives on subjects such as weapons and explosives. Court documents filed in Denver say Zazi was speaking with agents under an agreement where he might avoid prosecution.
He received the training in the federally administered tribal areas of Pakistan, the documents say.
Documents show authorities have kept a close eye on Zazi. FBI agents tapped his phones and kept him under surveillance earlier this month on a 30-hour drive from Colorado to New York, reports CBS News correspondent Don Teague. Authorities stopped Zazi twice during the drive - once near Kansas and again at the George Washington Bridge entering New York City.
In supporting documents filed with the court, federal investigators say a Sept. 11 search of Zazi's rental car in New York turned up a laptop computer that contained an image of nine pages of handwritten notes. Those notes included formulas and instructions about how to build explosives, detonators and other components of a fusing circuit, according to the affidavits.
Arrest Affadavit: Najibullah Zazi
Arrest Affadavit: Mohammed Wali Zazi
Arrest Affadavit: Ahmad Wais Afzali
Zazi was asked about the notes during FBI interviews last week and said he knew nothing about them, the documents said.
When asked about the handwritten notes allegedly found on his computer, Zazi allegedly told federal agents he hadn't written them and that he must have unintentionally downloaded it along with a religious book he downloaded in August. Zazi said he "immediately deleted the religious book within days of downloading it after realizing that its contents discussed jihad."
The FBI's court filings also say Zazi admitted to FBI agents last week that in 2008 he received al Qaeda weapons and explosives training at an al Qaeda training facility in Pakistan, near the border with Afghanistan
However, an arrest affidavit says the handwriting on the notes appeared to be Zazi's. The affidavit doesn't mention that they were part of a book, but that they were e-mailed as an attachment between accounts believed owned by Zazi in December, including an account that originated in Pakistan.
Listen: CBS News' Bob Orr with the latest on the arrests
"It appeared to be consistent with the handwriting as it appeared in the document," an FBI agent wrote of comparisons of Zazi's handwriting with the notes.
In addition, agents found Zazi's fingerprints on a scale and double-A batteries seized during a raid at a home in the New York City borough of Queens on Sept. 14.
Zazi, who lives in the Denver suburb of Aurora, underwent three days of questioning by the FBI before his arrest.
At the mosque Zazi attends in Aurora, Colorado, employees are expressing concern about the investigation.
"We are not terrorists - that's not our purpose here," said Sumay-ya Ezzaroualy, a mosque employee. "Our purpose is to bring peace and to share what we have."
Wendy Aiello, a spokeswoman for Zazi's defense team, says Zazi and his father were taken to FBI headquarters in Denver. Zazi's attorney, Art Folsom, met the father and son there late Saturday.
The Zazis were scheduled to appear in federal court in Denver on Monday, the Justice Department said. Afzali was to appear Monday in federal court in the Eastern District of New York.
If convicted, each would face eight years in prison.
Both Mohammed Zazi and Afzali face charges for allegedly lying to FBI agents about calls between Denver and New York. While prosecutors are seeking to detain Najibullah Zazi, prosecutors say they're not seeking detention for Mohammed Zazi, his father.
It was unclear from court documents whether officials would seek to detain Afzali, an Imam at a mosque in Queens who has worked as an informant for New York police.
Crews of journalists clustered outside Afzali's home in Queens. No one answered the doorbell at the three-story brick residence, adorned with brightly colored flower boxes.
To Alfazi's friends, the arrest came as a surprise. Muhammad Haji was planning to go to a mosque with Afzali on Sunday to celebrate the end of the Muslim holy month of Ramadan, reports CBS News correspondent Hari Sreenivasan in New York.
"He's a good person - that's all i can tell you," Haji said.
For years, Alfazi has been a source to for the New York Police Department. In a wiretapped conversation, Afzali told Zazi that the NYPD had come around with pictures and was looking for information on him. That was Sept. 10. One week later, authorities say, he lied about passing on that information.
"There's always a tension between wanting to arrest somebody and bring something down versus wanting to wait, let it unfold a little more, perhaps get other individuals," said Mike Balboni, a former homeland security advisor to the state of New York.
Before his arrest, Afzali told CBS Station WCBS in a phone call that he felt betrayed by the police.
"It's funny how for years they came to me … used to come to our house and drink tea. And then, they are going to set you up like this," he said Sept. 19.
"I think my client was arrested, because the government and the FBI is embarrassed," Alfazi attorney Ron Kuby told Sreenivasan. "This is a guy who's doing his best to help."
Carl Tobias, a law professor at the University of Richmond who has been tracking terrorist investigations around the country, said authorities could have made the arrests now because they feared too much information was getting out to the suspects. Additional charges could be filed later, he said.
FBI agents say Najibullah Zazi traveled to Pakistan twice this year on Jan. 15 and most recently on Aug. 28. Zazi says he was visiting his wife, who lives in the Peshawar region.
The investigation escalated after Zazi rented a car and drove from Denver to New York, crossing into Manhattan on Sept. 10. Zazi said he went to New York to resolve some issues with a coffee cart he owns in Manhattan, then flew home to Denver. The FBI searched Zazi's rental car and laptop during the New York trip and listened in on telephone conversations, according to the affidavits.
On Monday, FBI agents and police officers with search warrants seeking bomb materials searched three apartments and questioned residents in the Queens neighborhood where Zazi stayed.
An arrest warrant affidavit says FBI agents intercepted a phone conversation around Sept. 11 in which Afzali, a legal permanent resident from Afghanistan, told Zazi that he had spoken with authorities. "I was exposed to something yesterday from the authorities. And they came to ask me about your characters (sic). They asked me about you guys," Afzali told Zazi, according to the affidavit.
However, Afzali allegedly lied to authorities about that conversation when federal agents asked him about it Thursday, according to the affidavit.
The department says Mohammed Zazi, a naturalized U.S. citizen who was interviewed last week by the FBI, lied when asked if he knew anyone by the name of Afzali and said he didn't. The FBI said it had wiretapped a conversation between Mohammed Zazi and Afzali during Najibullah Zazi's visit to New York.
The FBI also searched Zazi's apartment and his uncle and aunt's home last week in suburban Denver. Authorities have not said what they found.
Zazi was born in Afghanistan in 1985, moved to Pakistan at age 7 and emigrated to the United States in 1999. He returned to Pakistan in 2007 and 2008 to visit his wife, according to Folsom.
At the mosque in Queens where Zazi recently visited, Masjid Hazrat Abu Bakr, worshippers marked the end of Ramadan on Sunday.
Zakir Khan said he had seen Zazi praying at the mosque recently, after not seeing him there for about a year. Zazi told him he was back in the city to get his coffee truck, to take it back to Colorado. Zazi spoke to Khan about his hopes of one day opening a limo business.
The New York Daily News reported Saturday that investigators spent several hours earlier this week at a U-Haul in Queens, where some men under scrutiny in the case tried to rent a large truck.
A manager at the rental lot, Robert Larson, told the newspaper the men went away empty handed because they didn't have a valid credit card. The paper reported that U-Haul workers identified one of the people involved in the rental attempt as Naiz Khan, an Afghan immigrant in Queens who knew Zazi and has been questioned by the FBI in connection with the case.
"I've never been to that U-Haul," he said Saturday. Asked what he thought about the scrutiny of Zazi, Khan said he wasn't sure.
"My opinion is, I don't know him. I know him from a mosque, that's all. He's my friend."