Destro's ancestor was tried, and sentenced to a life with a mask on his face. Destro kept it, and his face was burnt off, so CC gave it to him.
Now as for CC, Duke was marrying Baroness, and she had a brother named Rex, who was going into the army as well. Duke has him go into this complex to gain information, or something, but he has to hurry, because they're about to bomb the complex. Well, as luck would've had it, the planes came early, bombed the ^^^^ out of the complex, and everyone was led to believe that Rex had died.
Baroness went all depressed, Duke left her.....sad.
But, it turns out, Rex entered the base, and met up with this scientist, who showed Rex the Nano-Bots. He escaped the blask, but got a tad f-ed up. So he tried to use the nano bots to repair his face. Which then ruined his vocal cords and whatnot. So he joined up with Destro, recruited Baroness, and slowly took over Cobra.
See, he uses these nanobots to control people's lives. This is how he got all those soldiers on his side, and Destro.
So Rex = The Doctor = Cobra Commander. No mention of the hood, or mask. We only know he's CC because he asks Destro to call him "Commander..."
. Everytime I remember the Dungeons & Dragons movie with him playing a thief I cringe and now he's a Joe 
.
If you think Celine Dion is the only pain we can inflict upon you hapless yanks you've got another thing coming...
