G.I. Joe: The Movie messes with the show’s continuity, not just by introducing new characters and making one of them Duke’s half-brother, but by drastically changing the origin of Cobra Commander and Serpentor.
G.I. Joe: The Movie features several deleted scenes, a few that were animated and then removed, but most were in the final script and cut at the last minute.
The movie wasn’t the end, however, and even if it had been, this wasn’t an adventure that everyone could agree on.
The beginning of the movie focuses on Cobra, the cooler characters, and shows these new soldiers being efficient and deadly.