Major Nidal Malik Hasan, 42, could face the death penalty if convicted of carrying out the mass shooting at a processing centre where hundreds of soldiers were preparing to deploy to Iraq and Afghanistan.
The November 2009 incident is the worst shooting on a military base in US history. It shocked the military and led to an outcry for greater security from "homegrown" terror acts.
Hasan is also accused of wounding 32 fellow soldiers during the Fort Hood massacre - people who may end up being cross-examined by Hasan after he fired his lawyers and opted to represent himself.
Hasan wanted to use a "defense of others" strategy to justify his actions. But military judge Colonel Tara Osborn prohibited him from doing so after ruling that the argument had no merit.
In a copy of Hasan's intended opening statement obtained by AFP, he acknowledged that "it's not going to be easy" to convince a jury made up of soldiers that his actions were justified.
Hasan wrote that he planned to prove that the United States had engaged in an "illegal war" in Afghanistan and that "I did what I thought was necessary to help."
"I want to convey to you that my actions were meant to defend a people who were attacked by the United States," Hasan wrote.
"It took a lot of courage for me to help defend the Islamic Emirate of Afghanistan," he added.
It is not clear what Hasan will say when the court martial gets underway in a few weeks now that he has been barred from offering any evidence or testimony indicating he believed he was saving the lives of Muslims in Afghanistan when he admittedly opened fire.
Many military law experts agreed with the judge's ban, but Hasan's advocates argue that it violates his constitutional rights to a fair trial.
"I think that defense is obscene," said Richard Rosen, a military law professor at Texas Tech University. "That would justify shooting the president because he is targeting the Taliban and leaders of al Qaeda. It's offensive."
Rosen agreed with Osborn's recent ruling, which he said was "reasonable and not overly tough."
Hasan's former defense attorney John Galligan, a retired Army colonel, called the trial a "kangaroo court."
"She's essentially said you'll never hear from Nidal Hasan," Galligan told AFP. "It's a major, major error."
Hasan has managed to delay his trial with various legal manuevers and a lengthy battle over whether he could violate military rules by wearing a beard.
He raised the possibility of a further delay in May by firing his lawyers just days before jury selection was set to begin and then requesting a three-month delay to prepare his defense.
He withdrew the requested for a delay after Osborn barred the defense of others strategy.
Hasan has told the court he would like to plead guilty to all charges. However, US military law prevents a soldier from pleading guilty to capital charges unless the death penalty is waived.
An FBI review showed Hasan had been in contact with the US-born cleric Anwar al'Awlaqi, a key figure in al Qaeda in the Arabian Peninsula who was killed in a 2011 drone strike in Yemen.
Hasan, who was born in Virginia to Palestinian parents and raised in the eastern US state, had attended a mosque in 2001 where Awlaqi worked.
Hasan exchanged emails with Awlaqi in the months leading up to the shooting in which he questioned the morality of killing soldiers if they intended to attack Muslims. Awlaqi later called Hasan a hero.
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