Born in Burbank, California, Stones started with Disney training under animation veteran Eric Larson. He entered the Feature Animation training program three days after his college graduation in 1974. After animating a scene in The Rescuers, Stones moved into the story department on The Fox and the Hound. A brief stint at Walt Disney Imagineering followed, where he worked on Epcot's Transportation pavilion and the Imagination pavilion.

Stones worked at Disney for almost 30 years before leaving the company in 2003. In 2004, he started working at Universal Cartoon Studios, where he produced a direct-to-video feature about Brer Rabbit. Stones directed, produced and co-wrote with Mike Mignola Hellboy: Sword of Storms, the first of two direct-to-video animated films based on Mignola's popular comic book series Hellboy. Stones, a long time comic book reader, had worked previously with Mignola on developing Atlantis: The Lost Empire into an animated series. Hellboy: Sword of Storms made its television debut in the United States on October 28, 2006 on Cartoon Network. Hellboy: Blood and Iron, the second film in the Hellboy animated series, is scheduled to be screened on television in 2007.

He has also written "Pyramid of Death", one of the two stories in the first volume of the Hellboy Animated comic book adaptation.