11 years after the attack this comes to trial.They have been charged with terrorism, hijacking aircraft, conspiracy and murder in connection with the 11 September 2001 attacks in New York, Washington and Pennsylvania that killed nearly 3,000 people in 2001.
All could face the death penalty if convicted.
The decision to move to trial in a military court is the latest chapter in a decade-long political and legal battle over handling detainees.
One of the most contentious issues has been whether terrorism suspects like Mr Mohammed and his alleged co-conspirators should be tried in civilian courts as criminals or before military courts as enemy combatants.
The trial will bring a deep examination of the events leading up to 9/11, the deadliest attack ever carried out on United States soil and one that propelled the country into a global war against al-Qaeda and its affiliates.
The trial stands to be double-edged for President Barack Obama, who is running for a second term in November.
It will remind voters about the killing of long-fugitive al Qaeda leader Osama bin Laden last year, a highlight of his presidency.
But it could also draw attention to his failure to close the Guantanamo Bay prison, which he had promised to do as a candidate in the 2008 election.
The official overseeing the Guantanamo tribunals, retired Vice Admiral Bruce MacDonald, referred the case to a capital military commission on charges of terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians and other counts, the Pentagon said.
The case is fraught with controversy. All five defendants were held in secret CIA prisons before being sent to Guantanamo in 2006.
The CIA has acknowledged subjecting Mr Mohammed to a simulated drowning technique known as waterboarding during his interrogation, and other defendants have said they were abused.
The tribunals, which have gone through several revisions, ban the use of evidence gained through coercion, but critics say the hearsay rules are broad enough to allow the introduction of second-hand information obtained through torture.
9/11 was an event that impacted the entire world not just the US, I remember being in work that day (while in college) and watching it on a TV in the staff room, standing beside me a girl I worked with who broke down in tears as the first tower fell, it turned out that her uncle had recently taken a job for a company based in the World trade centre, he was one of the victims. I remember putting my arm around her trying to comfort her and thinking to myself, here we are in Dublin and the attack is in New York and this poor girl has lost someone very close to her.
My cousin Michael, and his brother in law's Chris and Dan (All marines) were shipped from the states to a base in Germany and then off to Afghan and Later Iraq, all 3 went career, (sadly Dan developed leukaemia a year or so ago so he is no longer active) but Chris and Michael are. Michael's helicopter was shot down in the opening weeks of the conflict in Iraq and he suffered injuries but that didnt stop him going back to work and doing what he was trained to do.
I've never fully agreed with the conflict in Afghan or Iraq, and me being me (as you all know) I'm never one to keep my opinions to myself, and I have had open discussions with them about the part they have played in the conflict and the number of innocent people who have been killed and the myth of WMD's. They have both answered the same way (perhaps its what they are told to say) "We didnt choose to go to Iraq or Afghan, we are soldiers, we follow orders, it doesnt matter if we agree with it but we have been asked to protect our country and if doing that means hunting down the suspects then thats what we'll do". I've always thought this a noble stance to take, even if I dont fully agree with it.
These two do not speak for the US Military forces so please dont take it as that.
I understand the hurt and anger many Americans feel over the events of 9/11, indeed as an Irishman I feel a degree of hurt and anger over the events of British rule in Ireland for so many years, but as we have seen the acts of a few do not consititute the beliefs of an entire nation.
What I can not agree with though is the decision to have a military trial on US soil. There is no way these men can have an fair trial, there is always a small chance that these are the wrong people and even if they are not they still deserve a fair trial.
Personally I feel they should face trial in The Hague.