Larry Hama provided character development for the series. He also wrote the file cards written on the back of the packaging of the G.I. Joe toy line. The files were short biographies of both the Joes and Cobra soldiers.
Writer and script editor Buzz Dixon had developed a story titled "The Most Dangerous Man in the World" which explored the origins of Cobra and introduced the previously unseen founder of Cobra, a political theorist who laid out the groundwork for the organization but was shunted aside by Cobra Commander. Before the script got past the outline stage, Hasbro informed Dixon that the second season was to feature the new character of Serpentor, the Cobra Emperor, and Dixon's idea was scrapped. He did however release his 'alternate history' as a downloadable book in 2016.
A large difference between the comic book and the cartoon is the fact that Storm Shadow switched sides and became a Joe in the comic, but remained loyal to Cobra throughout the initial run of the cartoon.
Plans were made to have the character Rocky Balboa join the G.I. Joe team in 1987. In fact, Marvel Comics "G.I. Joe: Order of Battle" issue #2 contained a dossier for Balboa and Hasbro designed a prototype figure with Sylvester Stallone's likeness. Additionally, a new character, Big Boa, was added to the Cobra roster, complete with boxing gloves, to act as Rocky's Cobra counterpart and foil. A deal could not be reached to use Stallone's likeness, however, and Marvel wound up retracting the Balboa dossier, instead deciding on Sgt. Slaughter to be G.I. Joe's trainer and "celebrity spokesman".
Sergeant Slaughter, a real-life professional wrestler, became a member of the G.I. Joe team during the show's second season. The real Sgt. Slaughter provided the voice for the animated character. The animated Sgt. Slaughter remained a member of the G.I. Joe team in later seasons, even after his real-life counterpart became an anti-American "heel" wrestler, teaming up with an "Iraqi General," General Adnan, against Hulk Hogan at Wrestlemania VII during the time of the 1990 Persian Gulf War.