Rezwan Ferdaus, 26, was arrested and charged with the aerial bombing plot to attack Washington and attempts to deliver bomb-making materials for use against US troops in Iraq, US Attorney Carmen Ortiz said in Boston.
"The conduct alleged today shows that Mr Ferdaus had long planned to commit violent acts against our country, including attacks on the Pentagon and our nation's Capitol," Ortiz said.
During the alleged plot, undercover FBI agents posed as al Qaeda-linked accomplices who supplied Ferdaus with one remote-controlled plane, C4 explosives, and small arms that he allegedly envisioned using in a simultaneous ground assault in Washington.
The plan, according to the criminal complaint, was to strike the Pentagon and the Capitol's famous white dome and "decapitate the entire empire. (It will be the) final nail in the coffin”.
However, "the public was never in danger from the explosive devices, which were controlled by undercover FBI employees," the FBI said.
Ferdaus was arrested in Framingham, near Boston, immediately after putting the newly delivered weapons into a storage container, the FBI said.
Authorities described Ferdaus as a physics graduate from Northeastern University who was an enthusiastic fan of al Qaeda and had been committed to "violent jihad" since early last year.
He also apparently possessed a knack for technical work.
Ferdaus is accused of modifying mobile phones for use as electrical switches in bombs to be used against US troops in Iraq.
"That was exactly what I wanted," he is alleged to have said when told -- falsely -- that one of his phones had been part of a bomb that killed three soldiers.
Aided by the FBI undercover team, Ferdaus was also developing far more grandiose plans, according to the authorities.
"Ferdaus stated that he planned to attack the Pentagon using aircraft similar to 'small drone airplanes' filled with explosives and guided by GPS equipment. According to the affidavit, in April 2011, Ferdaus expanded his plan to include an attack on the US Capitol," the FBI said.
The planes were large enough to carry "a variety of payloads (including a lethal payload of explosives), can use a wide range of take-off and landing environments, and fly different flight patterns than commercial airlines, thus reducing detection," according to the criminal complaint filed in court.
In May and June 2011, Ferdaus delivered thumb drives to the undercover team with step-by-step plans for his alleged plot.
This included using three remote-controlled planes and six people who would be armed with Kalashnikovs and grenades.
The plan, according to the FBI, was to use the "aerial assault" to "eliminate key locations”.
The Capitol's dome would be blown "to smithereens”, Ferdaus was quoted in the complaint as saying.
At that point the attackers would herd survivors into a tight corner and "open up on them" and "keep firing”.
"It ought to result in the downfall of this entire disgusting place," Ferdaus is alleged to have said.
Republican lawmaker Peter King, chairman of the House Committee on Homeland Security, said the arrest was a reminder that 10 years after the 9/11 attacks, al Qaeda and its sympathisers "remain committed to attacking the US homeland”.
The New York congressman said it "also underscores the need to continue efforts to combat domestic radicalization and the evolving threat of 'lone wolf' extremists."
Ferdaus made a first court appearance before a federal judge in Worcester, Massachusetts, on Wednesday and was scheduled for a detention hearing on Monday.
If convicted, Ferdaus faces up to 15 years in prison for supporting a foreign terrorist organisation, up to 20 years for attempting to destroy national defence sites, and the same again for attempting to use explosives against buildings owned by the United States.
