Storm Shadow returns!Okay, maybe not a WMG per se; you can't really kill him off after just one installment. But! After being stabbed and falling into the icy arctic waters, Storm Shadow floats down, his bodily functions slowing as he descends into hypothermia. Of course, he's Arashikage. So he uses the Sleeping Phoenix to temporarily suspend his life, allowing him to continue to exist as the explosion of the underwater base throws him onto the ice-sheet. He is found by Cobra Commander, who isn't one to waste resources, and revived along with a good dose of mind-controlling nanobots. Storm Shadow then shows up in the sequel, brainwashed but with a Heel-Face Turn totally possible.
The Baroness didn't fight off the Nanomites.They're still inside her and working absolutely perfectly. Cobra Commander is just using her as another The Mole, so she can free him and Destro in time for the next movie.
Storm Shadow didn't kill the master.Despite the change in age and having a sword rather than an arrow, the story is verbatim to the comics: Hard Master is found killed by Storm Shadow's weapon and Stormy runs away, everybody believes Stormy did it due to his jealously of Snake-Eyes. In the original comicbooks, the real killer was Zartan, long story, but my guess is that the killer in the movie version was Firefly and he will appear in the sequel.
Cobra Commander is Tom HansenTom Hansen meets Autumn, but it ends up badly. So bad, in fact, that it started his descent into darkness.
The upcoming sequel will contain "Renegades" in it's title.G.I. Joe: Renegades is being put on hiatus due to possible brand confusion with the movie's sequel. If the sequel is called, say, "Renegades of Cobra", unaware viewers might think its in the same continuity as the cartoon, which it isn't. Having two continuities use the same word? Can't have that.
Storm Shadow is an assassin. From assassin's creed.