No doubt, when the 35-year-old French citizen of Moroccan origin was indicted 21 months ago, many people thought the case would be over by now.
The case has become bogged down in a legal debate over whether the defendant can get a fair trial while the US Government refuses to allow him access to particular witnesses for national security reasons.
The US Constitution has emerged as an obstacle to the Justice Department's efforts to prosecute Mr Moussaoui.
The Sixth Amendment of the Constitution guarantees access to witnesses and other evidence to ensure a fair trial.
However, the witnesses Mr Moussaoui wants to hear evidence from are being held at undisclosed locations by the US military and are undergoing sensitive interrogation.
Mustafa Ahmed al-Hawsawi, believed to be an al-Qaeda financier.
The BBC's security correspondent Frank Gardner says the whole interrogation process is highly classified.
"The military don't want to blow ongoing operations in the drive to wrap up the leadership of al-Qaeda," our correspondent says.
Ramzi Binalshibh is being held at a secret location
"They don't want information spilling out in a court in Virginia, in fact, they want to keep lawyers as far away as possible."
According to some experts, interrogators need to sustain a psychological advantage over the detainees by depriving them of all contact with the outside world.
But the judge presiding over the Moussaoui case in Virginia, Leonie M Brinkema, has already ruled that the Justice Department should allow the defendant to hear the detainees' evidence through a satellite hook-up.
In particular, Mr Moussaoui wants to hear evidence from Ramzi Binalshibh.
Defence court documents argue that statements made by Mr Binalshibh to his interrogators would help show that Moussaoui was "a problematic and unstable hanger-on who could never be trusted to be a participant in any significant undertaking by al-Qaeda and was not a participant in the plan for the 11 September attacks".
Human rights fears
The government's continued refusal to allow evidence from the detainees could now lead to the charges against Mr Moussaoui being dismissed.
In that case, Mr Moussaoui could find himself being designated an "enemy of the state" and appearing before a military commission.
The government has said that if it is unable to get a court to recognise the need to protect national security in this case, it will have no choice but to put Mr Moussaoui before such a commission.
A US legal expert, Professor Scott Silliman, says the government is trying to negotiate a legal maze in an environment that has changed massively in the past two years.
The law in question is the Classified Information Procedures Act, under which classified information in federal courts is normally handled.
The Act allows the Justice Department to appeal against Judge Brinkema's decision to allow Mr Moussaoui access to the witnesses.
But once the appeal is lodged, the judge can take sanctions against the Justice Department, such as dismissing the case.
This is precisely what the government wants, because it will allow the case to proceed to the appellate court quickly.
If the court rules in favour of the Justice Department, Mr Moussaoui will be re-charged.
If it does not, the government has threatened to try him by a military commission.
"I believe the military trial threat is just rhetoric to pile on the pressure," says Professor Silliman, who heads the Center on Law, Ethics and National Security at Duke University, North Carolina.
"It would send out the wrong signals at a time when the US is under attack by members of the international community.
"It implies that the government is unable to get justice in a criminal court and that it is easier to get a conviction in a military commission."
At the time of his indictment, the government asserted that Mr Moussaoui would receive swift justice in an open court. This would show the world how fair the US judicial system was.
Now the administration is in danger of being accused by critics and human rights groups of trying to set a dangerous precedent - that important constitutional rights can be taken away in terrorism cases.
"We are concerned that the government is trying to circumnavigate normal criminal justice procedures," Amnesty International's spokesman Neil Durkin told BBC News Online.
"And we are also becoming alarmed at the growing trend to have people classified as enemy combatants and moving such cases into the sphere of military justice."