The updated indictment accuses Mohammed Wali Zazi of witness tampering and lying to the FBI in an alleged cover-up of the foiled scheme.
The 54-year-old Zazi, who lives in a Denver suburb and is free on bail, previously pleaded not guilty to conspiracy to obstruct justice. He's due back in federal court in Brooklyn on Dec. 9 for arraignment on the new charges.
"From our perspective, this does not change anything," said defense attorney Deborah Colson, adding that Zazi intends to pleaded not guilty again.
"We intend to fight it, to take the case to trial," she said. "He is looking forward to his day in court."
The Afghan immigrant's son, Najibullah Zazi, has pleaded guilty and is cooperating in an ongoing investigation of the plot and it roots in Pakistan, where Zazi and former friends from high school allegedly traveled in 2008 to seek terror training from al-Qaida.
Zazi, a Colorado airport van driver, admitted that once back from Pakistan, he tested peroxide-based explosive materials in a Denver suburb before traveling by car to New York intending to attack the subway system to avenge U.S. military involvement in Afghanistan.
Prosecutors say the two friends, Adis Medunjanin and Zarein Ahmedzay, agreed to join Zazi last year in what prosecutors described as "three coordinated suicide bombing attacks" on Manhattan subway lines. The would-be attacks were timed for days after the eighth anniversary of the Sept. 11 terror attacks.
The plot was disrupted in early September when police stopped Zazi's car as it entered New York.
FBI agents arrested Zazi's father on obstruction charges, alleging he conspired with others to destroy or hide "glasses, masks, liquid chemicals and containers" that were evidence in the case.
The new indictment has additional obstruction counts, along with a charge alleging the elder Zazi lied when he denied having a telephone conversation with a Queens imam about his son being in trouble. It also alleges he supplied false information for an asylum application for his nephew.
Ahmedzay has pleaded guilty. Medunjanin is fighting terrorism charges.