Hernandez has been charged with two counts of first-degree murder and other offences in the July 2012 killings of Daniel de Abreu and Safiro Furtado. A third man was wounded in that attack.
An indictment Thursday places the gun in Hernandez's hands weeks before he signed a five-year, $40 million contract with the Patriots and went on to catch 51 passes and score five touchdowns during the 2012 NFL season.
Hernandez, 24, has pleaded not guilty in the killing last year of Odin Lloyd, 27, a semi-pro football player whose body was found in an industrial area near Hernandez's home in North Attleborough. He was released by the Patriots last summer after being arrested in Lloyd's death.
His attorneys, Charles Rankin and James Sultan, said their client was looking forward to his day in court on the latest charges. "It is one thing to make allegations at a press conference, and another thing to prove them in a courtroom," they said in a statement.
According to Suffolk District Attorney Daniel Conley, the night of the 2012 shootings unfolded when Hernandez and an associate went into the Cure Lounge at about the same time as the other men. The prosecutor would not describe what he called their "chance encounter," but said there was no evidence that Hernandez knew the victims beforehand.
After the men left, Hernandez followed in an SUV and pulled up alongside the men as their vehicle was stopped at a red light in Boston's South End, Conley said.
"Aaron Hernandez fired a .38-calibre revolver multiple times from the driver's side of his vehicle into the passenger's side of the victim's vehicle," killing de Abreu, 29 and Furtado, 28, Conley said.
The case remained unsolved for months, but following the Lloyd shooting, Conley said the SUV was found in Bristol, Connecticut, where Hernandez grew up, and the gun used in the double shooting was recovered from a person with ties to Hernandez. Previous court documents have said the vehicle was found at the home of Hernandez's uncle.
Conley would not say whether prosecutors suspected a link between the two cases beyond their accusations of Hernandez's involvement.
A spokesman for the Patriots said the team had no comment.
Families of the victims in the Boston shooting have filed civil lawsuits against Hernandez seeking $6 million for the wrongful deaths of the two men.
Hernandez was expected to be arraigned on the new charges in Suffolk Superior Court next week.
Associated Press writer Paige Sutherland and sports writer Jimmy Golen contributed to this report.