The series was written for most of its 155-issue run by writer, artist, and editor Larry Hama, and was notable for its realistic, character-based storytelling style that was unusual for a toy comic at the time. Hama worked closely with the series artists, providing them with sketches of the characters and major scenes. While most stories involved the G.I. Joe team battling against the forces of Cobra Command, an evil terrorist organization, many also focused on the relationships and back stories of the characters.
The first issue was published in June 1982, containing two stories, both of which were written by Hama. The first story, "Operation: Lady Doomsday", was drawn by Herb Trimpe, who drew most of the early issues and also wrote issue #9; and the second story, "Hot Potato", drawn by Don Perlin. This issue introduced many basic concepts of the G.I. Joe universe, such as the Joes having a base under a motor pool, and introduced the iconic 'original 13' G.I. Joe Team members. The issue also introduced two recurring villains, Cobra Commander and the Baroness. Whereas Cobra Commander and the various Joes already had action figures issued, The Baroness was the earliest example of a G.I. Joe character whose first appearance in the comics predated the conception of their action figure.
Most of the early stories were completed in one issue, but multi-part stories began to appear by the middle of the series' first year of publication, and there were hints of the ongoing storylines that would later characterize the series. In May 1983, issue #11 introduced many new characters, including most of the 1983 action figure line and the villain Destro, who would become a frequently recurring character. Many subsequent storylines involved the machinations and power struggles between him, Cobra Commander, and the Baroness. Issue #11 established a pattern for the series in which every so often Marvel would publish an issue introducing a group of characters and vehicles that represented the new year's toy offerings. In 1986 echoing events portrayed in the TV series, G.I. Joe #49 was published introducing the character of Serpentor, a genetically created amalgam of history's greatest warriors. Serpentor played a significant role in the Cobra Civil War, which occurred in issues #73-76, a landmark story event that involved nearly every extant G.I. Joe and Cobra character vying for control of Cobra Island.