The publishing of a second regular G.I. Joe series proves just how popular the original series had been. Each issue featured a standalone story having little to do with the storyline of the main series. Cobra appeared in less than half of the issues, which usually focused on the Joes' other anti-terrorist activities. The plots tended to be more serious, more realistic and often more violent. Nearly every issue was written by Larry Hama with art by Herb Trimpe, who worked on many of the earliest issues of the regular series and the entire Order of Battle miniseries. The Special Missions was first published bi-monthly, but went monthly until its 28th and final issue. The first Special Missions story appeared in the double-sized G.I. JOE #50, two months before the series began. In 2006, Devil's Due Publishing began to release a new series of Special Missions one-shot comics.

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