Kahton Anderson, 14, inadvertently shot a 39-year-old man riding the bus home when he fired at another teenager, police reported.
The eighth-grader flashed a .357 revolver on the B15 bus crossing from Clinton Hill to Bedford-Stuyvesant in Brooklyn on March 20.
Anderson was prosecuted as an adult after the victim, Angel Rojas, later died from his injuries, and was indicted on second-degree murder charges Wednesday.
Anderson's father, referred to only as Mr. Anderson, offered his apologies to Rojas' family but stressed his son's youth.
"Kahton is a child, who thinks like a child. Kahton's a tall child. He's a boy; I'm a man," Mr. Anderson said outside the Brooklyn courtroom, according to The New York Times.
Rojas "did not deserve to die so tragically, and we will hold the defendant Kahton Anderson responsible for taking the life of this innocent and hard-working man," said Brooklyn district attorney Kenneth P. Thompson.
Police said the shooting was a petty turf war between "crews" of almost-teenage children, which, police say, now account for 30 percent of all shootings in the city.
The bus incident involved a rivalry with the Twan Family, part of the Marcy House crew. Anderson shot off his gun when he thought a Mercy member was reaching for his.
Anderson is part of the crew Stack Money Goons located at the Tompkins Houses, where some of his schoolmates lived. Despite his gang affiliation, fellow Middle School 57 classmates did not think of Anderson as a violent person.
"Kahton, you wouldn't think he'd have a gun," Katoya Williams, 14, said. "Of all the boys, I wouldn't expect him to have one. He's real decent."
But Anderson was constantly in trouble at school, school officials say, sometimes for violating school uniform or talking during class, but there was a school suspension and sealed arrest in 2011.
"There is no 'for,' there is no common purpose, there is no goal. It's basically survival, it's basically safety, it's protection," said Shanduke McPhatter, a former member of the Bloods who now runs an anti-gang outreach group, said of gangs.
