It seems that the script for the sequel of G.I. Joe: The Rise of Cobra has been complete according to Hasbro CEO Brian Goldner as reported by MTV News. While a director has not been found yet, there has been reports that both F. Gary Gray who directed The Italian Job and Jon Chu who directed Step Up 3D & Never Say Never are in the potential list.
And if you are wondering about the link between the two films, it has something to do with ending of the first film:
"Obviously, we know coming out of the first film that the president is an impostor," Goldner explained. "You might begin with the knowledge of having your president as an impostor. What would that mean? From that, you can tell a very big story without only having to rely on the chronology of the first film."