Ahmed Omar Abu Ali, 23, a U.S. citizen, had been held without charges in Saudi Arabia since June 2003. He was returned to the United States and made an initial appearance in U.S. District Court shortly after his arrival.
He did not enter a plea but contended he was tortured while detained in Saudi Arabia and offered through his lawyer to show the judge his scars.
Before the indictment, a lawsuit filed on behalf of Abu Ali claimed U.S. officials had Saudi authorities detain him so he could be harshly interrogated. Federal prosecutors have been fighting attempts to get the government to disclose why he was being held in Saudi Arabia.
According to the indictment, Abu Ali discussed Bush-assassination plans with an unidentified al Qaeda member in 2002 and 2003, while Abu Ali was attending college in Saudi Arabia.
They discussed two scenarios, the indictment said, one in which Abu Ali "would get close enough to the president to shoot him on the street" and, alternatively, "an operation in which Abu Ali would detonate a car bomb."
While the indictment does not identify the conspirator, it says he was one of 19 people publicly identified by the Saudi government in 2003 as terrorists.
The only other detail of the alleged plot in the indictment states that Abu Ali received a religious blessing from another unidentified conspirator to assassinate the president.
U.S. Attorney Paul McNulty said in a statement that "after the devastating terrorist attack ... of Sept. 11, this defendant turned his back on America and joined the cause of al Qaeda. He now stands charged with some of the most serious offenses our nation can bring against supporters of terrorism."
Abu Ali's parents insist their son was tortured for almost two years in a Saudi Arabian prison and has the scars to prove it, reports CBS News Correspondent Jim Stewart.
"Regarding this plot about our president, it's a joke. It's more lies. I can just say because my son was tortured these indictments came. It's lies over lies," said his mother, Faten Abu Ali.
Abu Ali's indictment is just the latest in a series of cases involving alleged foreign detention and torture that have deeply troubled U.S. courts.
"He was there in Saudi Arabia," says CBS News Legal Analyst Andrew Cohen. They were evaluating him and they were essentially keeping him on ice until the federal government was willing to do something with him."
Cohen notes that the curious case is a to arise since Sept. 11, 2001.
"It's a little bit John Walker Lindh, the so-called "American Taliban." It's a little bit Zacarias Moussaoui, the al Qaeda foot soldier the feds still can't get to trial. It's a little bit Yaser Esam Hamdi, the "enemy combatant" who last June won a big ruling from the Supreme Court,'' said Cohen. "And it's a little bit Guantanamo Bay, where detainees are fighting to have federal courts recognize whatever rights they may have."
In Abu Ali's case, the government apparently relied on information gathered by the Saudis to charge that he discussed with al Qaeda operatives plans to "shoot [President Bush] on the street" or "detonate a car bomb" near him.
The indictment also charges Abu Ali tried to enlist in the fight against U.S. forces in Afghanistan, received money from al Qaeda to buy a computer and planned to start up an al Qaeda cell once back in the U.S.
But from the day he disappeared into Saudi custody in June 2003, Abu Ali's family has been fighting to get him back to the U.S. and face the judicial process here.
And last fall the family's attorney filed an affidavit charging an assistant U.S. Attorney seemed aware Abu Ali was being tortured overseas. In reply to a question, the U.S. Attorney allegedly "smirked and stated, 'He's no good for us here. He has no fingernails left,'" according to the affidavit. A government spokesman declined comment on the charge.
On Tuesday, more than 100 friends and family jammed the courthouse to show their support for Abu Ali. Many of them laughed in the courtroom when government lawyers described the alleged assassination plot.
Abu Ali's lawyer, Edward MacMahon, said after the hearing that his client will plead innocent. MacMahon said he saw the scars on Abu Ali's back and accused the government of relying on information obtained through torture.
"He expects a fair trial in which he will be vindicated," MacMahon said. "Evidence that comes through torture is the most unreliable evidence."
During the hearing, Abu Ali asked to speak to the judge. U.S. Magistrate Liam O'Grady suggested he consult with his attorney, who then relayed Abu Ali's claims of torture.
When Abu Ali offered to show the judge his back, O'Grady said that he be able to do so on Thursday at a detention hearing, in which his lawyers will seek his release pending trial.
"I can assure you you will not suffer any torture or humiliation while in the marshals' custody," O'Grady said.
Abu Ali was born in Houston and moved to Falls Church, a Washington suburb. He was valedictorian of the Islamic Saudi Academy in nearby Alexandria, Va.
"He was very wise, very mature for his age," said Jamal Abdulmoty, who knew Abu Ali through their shared involvement in northern Virginia's Muslim community. "We cannot imagine" that he would be involved in an assassination plot.
Abu Ali is charged with six counts and could face a maximum of 80 years in prison if convicted. The charges include conspiracy to provide material support to al Qaeda, providing material support to al Qaeda, conspiracy to provide support to terrorists, providing material support to terrorists and contributing service to al Qaeda.