The story unfolded on May 29 near the Dearborn Drive and Old Oxford Road in north Durham.
Investigators said they believe his school bus driver may have coordinated the attack while driving the bus.
Authorities wrote in the search warrant that the bus driver had gotten into a fight with one of the boy's relatives before the shooting.
Police said security video from school bus No. 611 show the bus driver exchange derogatory words with the teenager before the shooting.
According to investigators, the video also shows the driver texting throughout the bus route and just as the student gets off the bus.
ABC11 is not naming the suspected bus driver, because the driver has not yet been charged with any crime.
Durham Public Schools said the substitute driver was fired the following day for not reporting the incident and for texting and driving.
"Our bus drivers as a group are committed to keeping students safe on the road and at bus stops. We will not accept any conduct by a school bus driver that does not uphold this commitment."