What was Destro supposed to be?
I mean, his head apparantly was made of metal, but his faced moved like a normal human face. What the hell was that about?
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It was a metal mask (beryllium steel) to honor his family's tradition (Destro clan), which was a ritual started by when an ancestor was caught selling weapons for both sides (English Civil War) and forced to wear a mask for his crime (think Man in the Iron Mask), they didn't execute him or imprison him behind bars because they needed his weapons (I think it was something to do with witchcraft in the cartoon, instead of selling weapons to both sides). The Destro clan continued the tradition of historically selling weapons to any and all persons or organizations for the most part.
Destro is not an employee of Cobra, but is a trusted lieutenant and very powerful in the organization (The Baroness is the second-in-command with Cobra, misconception that Destro is), but merely a committed business partner and a power grabber of sorts (He most certainly wants Cobra for himself, as shown in many incarnations of GI Joe), since he does good business with Cobra, though in the comics and sometimes in the TV shows, he will very quickly switch sides, if it is good for business.
In the comics, the Baroness may be the second in command, but the cartoon almost certainly places Destro in that position. And, yeah, they made Destro's ancestors practitioners of witchcraft.
There were a couple of changes made in the crossover, such as Duke and Scarlet being an implied couple.