The 41-year-old republican, from Lurgan, Co Armagh, was remanded in custody charged with the murders of Mark Quinsey, 23, of Birmingham, and Patrick Azimkar, 21, of London, who were shot dead at the gates of Massereene Barracks, Antrim, on Saturday, March 7, while they collected pizzas from delivery men.
Mr Duffy was also charged with five counts of attempted murder — of three soldiers and two delivery men — and possession of arms and ammunition with intent. Mr Duffy appeared in the dock handcuffed to a police officer.
PSNI Detective Chief Inspector Jeffrey Smyth told the court that: “My evidence in this case relies on three planks. The first is forensic evidence, the second is CCTV and the third is witness evidence.”
He added that DNA evidence found in the car used by the killers in their getaway linked Mr Duffy to the killings.
He said: “This is not trace elements — this is a full DNA profile. It was inside a latex glove found on the floor of the Vauxhall Cavalier.” He conceded later that only the tip of the glove had been found.
Mr Duffy will remain in custody until a further hearing on April 21, when he will appear by video link. Mr Duffy was not asked to enter a plea but his lawyer Pat Vernon said outside the court his client would deny the charges.
Outside the court loyalists hurled abuse when Mr Duffy was driven away.
Earlier this week, Mr Duffy was one of six suspects who won a challenge against their detention under British anti-terrorist laws, however he was immediately rearrested.
Mr Duffy is one of the North’s most high-profile dissident republicans.
He was initially seen as a supporter of Sinn Féin President Gerry Adams’ endorsement of the peace process, only breaking with the provisional republican movement in recent years.
In recent months Mr Duffy was associated with the republican political campaign group Éirígí, which broke away from Sinn Féin in 2006.
However when Mr Duffy was initially arrested on March 14, Éirígí spokespeople confirmed speculation that he had ended his membership of the group.
On Thursday night scores of people attended a protest meeting in Lurgan in support of Mr Duffy.
At the meeting Éirígí spokesman Breandan Mac Cionnaith said Mr Duffy had been refusing food.
His brother Paul Duffy said his weight had dropped from 12st 2lbs to 11st since he was first arrested. Referring to his brother’s “hunger strike”, Paul Duffy said: “He is determined to see it through, and if I know Colly, he will go all the way.”