Stones worked at Walt Disney Television Animation since its formation in 1984. He was one of the creative forces behind many of the Disney Afternoon shows of the late 1980s and early 1990s. He was one of the producers of Chip 'n Dale Rescue Rangers and Disney's Adventures of the Gummi Bears (third season only). In 1990, Stones was asked to develop an original concept inspired by two episodes of Ducktales; he illustrated what would eventually become known as Darkwing Duck. Stones wrote and produced the pilot film for the show, Darkly Dawns the Duck, which premiered in April 1991. After the success of the pilot, Stones served as writer and producer of the show until the end of its run in late 1992. According to an interview, the character of Gosalyn Mallard was partly based on what he believed his then two-year-old daughter would be like when she grew older.
After Darkwing Duck, Stones served as director in Aladdin, a television series based on the original film. In 1994, he co-wrote, produced and directed The Return of Jafar, a direct-to-video sequel to the 1992 film Aladdin. He also directed and produced a second sequel to Aladdin in 1996, Aladdin and the King of Thieves. The film marked the end of the Aladdin films and the Aladdin animated series.
In 1998, Stones served as executive producer of Hercules: The Animated Series. Two years later, he directed the direct-to-video film Buzz Lightyear of Star Command: The Adventure Begins. The film served as pilot episode to the 2000 television series Buzz Lightyear of Star Command, which Stones also produced. In 2003, he directed Atlantis: Milo's Return, the direct-to-video sequel to the film Atlantis: The Lost Empire.
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, was 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.