The victims in the 2012 killing, Daniel de Abreu and Safiro Furtado, were shot to death in a car as they waited at a red light on a July night in Boston's South End neighborhood.
Suffolk District Attorney Daniel Conley would not elaborate on what happened in the nightclub, other than saying that the encounter "triggered a series of events that ended in the murders." But he said that after the men left, Hernandez followed in an SUV, then pulled up alongside the vehicle and fired multiple shots from a .38-caliber revolver into the passenger's side, killing de Abreu and Furtado, and wounding a third man. Two other passengers in the car were uninjured.
Conley said there was no evidence that Hernandez knew the victims prior to that evening.
Weeks after the double shooting, Hernandez signed a five-year deal worth about $40 million with the New England Patriots and went on to play in 12 games that season. A spokesman for the Patriots said the team had no comment.
Hernandez is already awaiting trial in the June 2013 shooting death of 27-year-old Odin Lloyd near Hernandez's North Attleborough home and is being held without bail after pleading not guilty to murder in Lloyd's death.
"Under our system of justice, Aaron Hernandez is innocent of these charges, and he looks forward to his day in court," said his lawyers, Charles Rankin and James Sultan, in a statement. Alluding to a news conference held by Conley to announce the charges, the attorneys said they would not try the case in the media.
Conley said the investigation of the Boston killings moved forward after the Lloyd case, which will be tried separately in another Massachusetts court. He noted the discovery in Bristol, Connecticut, of the car Hernandez was driving the night the men died and the recovery of the alleged murder weapon from an unnamed person with ties to Hernandez.
Conley declined to say whether authorities suspected any connection between the Boston and North Attleborough shootings.
Hernandez is charged with two counts of first-degree murder and three counts of armed assault with intent to murder, as well as unlawful possession of the gun used in the attack.
Conley said the notoriety surrounding the former tight end played no role in the way the case was investigated.
"This was never about Aaron Hernandez. This case was about two victims who were stopped, ambushed and senselessly murdered on the streets they called home," he said.
Tanya Singleton, Hernandez's cousin, was charged with criminal contempt of court in the indictment returned by a Suffolk County grand jury. Singleton was given immunity to testify before the grand jury but refused, Conley said.
A message left with Singleton's lawyer was not immediately returned.
Families of the victims have filed civil lawsuits in February against Hernandez seeking $6 million for the wrongful deaths of the two men.
He is expected to be arraigned on the new charges in Suffolk County Superior Court next week.
Hernandez was cut by the Patriots hours after his arrest in the Lloyd case, and coach Bill Belichick later said he was "shocked and disappointed" upon learning of the criminal investigation.
Thursday's indictment raises the possibility that Hernandez played the 2012 NFL season after killing the two men.
Six weeks after allegedly committing the murders in July 2012, Hernandez received the lucrative contract extension from the Patriots and talked about being inspired by his family to make smart decisions.
"I called [my family] and told them obviously what the contract was, and the basics about it," he said at the team's annual charity gala on Aug. 27, 2012. "They were all crying. I was crying right with them. This is probably one of the best days of my life. I'll remember this day forever. I just hope I keep going, doing the right things, making the right decisions so I can have a good life, and be there to live a good life with my family."
Upon receiving the deal, Hernandez donated $50,000 to a fund Patriots owner Robert Kraft set up to honor his late wife, Myra, and told reporters he would "live life as a Patriot."
"[Kraft] didn't need to give me the amount that he gave me, and knowing that he thinks I deserve that, he trusts me to make the right decisions, it means a lot," Hernandez said then. "It means he trusts my character, and the person I am, which means a lot, because my mother, that's how she wanted to raise me.
"They have to trust you to give you that money. I just feel a lot of respect and I owe it back to him. Not only is it $50,000 ... it's more, I have a lot more to give back, and all I can do is play my heart out for them, make the right decisions, and live life as a Patriot."
Also Thursday, Ernest Wallace, an associate of Hernandez, pleaded not guilty to murder in the shooting death of Lloyd.
Information from ESPNBoston.com and The Associated Press was used in this report.
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