The discovery came amid an intense manhunt after prosecutors say the 35-year-old went on a rampage Monday at three homes a few miles apart.
It was the second major manhunt to transfix Pennsylvania in recent months. Eric Frein spent 48 days at large in the Poconos after the September ambush slaying of a state trooper.
Stone's neighbors say they're relieved he can't harm anyone else.
His former wife, 33-year-old Nicole Stone, was found dead after a neighbor saw Brad Stone fleeing just before 5 a.m. Monday with their two young daughters.
Police then made the grim discovery of five people killed in two other houses: Nicole Stone's sister, brother-in-law and 14-year-old niece were dead. A 17-year-old nephew was left clinging to life. And her mother and grandmother had been fatally shot.
Brad Stone and his ex-wife had been locked in a court fight over their children's custody since she filed for divorce in 2009. He filed an emergency motion early this month, although the resulting Dec. 9 ruling remains sealed in court files.
"She would tell anybody who would listen that he was going to kill her and that she was really afraid for her life," said Evan Weron, a neighbor at the Pheasant Run Apartments in Harleysville.
He said Nicole Stone would talk frequently about the custody dispute.
"(Nicole) came into the house a few times, a few separate occasions, crying about how it was very upsetting to her," Weron said.
Neighbors woke to the sounds of breaking glass and gunshots coming from Nicole Stone's apartment early Monday. They alerted authorities after seeing her ex-husband racing away with the children. The girls later were found safe with his neighbors, Montgomery County District Attorney Risa Vetri Ferman said.
SWAT teams surrounded his Pennsburg home for hours on Monday and pleaded through a bullhorn for him to surrender.
Later that night, police in neighboring Bucks County swarmed an area outside Doylestown after an attempted carjacking by a man dressed in fatigues and similar in appearance to Stone.
The rampage started in Souderton at the home of Brad Stone's former sister-in-law and ended about 90 minutes later at Nicole Stone's apartment in nearby Harleysville, Ferman said.
Nicole Stone's sister, Patricia Flick, her sister's husband, Aaron Flick, and the couple's 14-year-old daughter, Nina Flick, were killed in the first wave of violence, which was not discovered until nearly 8 a.m. Their 17-year-old son, Anthony Flick, was pulled from the house with a head wound and was taken in an armored vehicle and then by helicopter to a Philadelphia hospital for treatment.
Nicole Stone's mother, Joanne Hill, and grandmother Patricia Hill were killed next at their home in nearby Lansdale. Investigators were alerted by a hang-up call to emergency dispatchers, Ferman said.
Then they got the call from Nicole Stone's neighbors.
Harleysville, Lansdale and Souderton are within a few miles of each other.
"I'm (angry) because he could have come to my door and I could have taken him to a treatment center, and we could have worked this out," said longtime friend Matthew Schafte.
He described Stone as a Marine veteran who served in Iraq, but said he was not aware of any resulting injuries.
"He was pumped to go into the military," said Schafte, who said his friend was a fixture at a local American Legion post, both before and after his service.
His wife, Tina Bickert Schafte, said she had babysat for both Nicole Stone and her sister Patricia when they were growing up.
Brad and Nicole Stone married in 2004 and filed for divorce in 2009, court records show. Nicole Stone became engaged over the summer, neighbors said.
He had faced several driving-under-the-influence charges, one of which was handled in veterans' court and led to a three- to 23-month sentence.
Brad Stone remarried last year, according to his Facebook page and court records, and has an infant son. Neither his wife nor the son were injured. His wife's Facebook page shows their son and Stone's daughters having their picture taken with Santa on Saturday.