It seems that some people weren't able to follow what was going on.
Destro was in charge of MARS not COBRA. CC took down MARS, took revenge on Destro for what happened to him, and has the pieces in place to strike against GI Joe and try and take over the world.
The barroness is evil, the nanomites are what took her over to make her "good". This is the very reason why hers were designed to be near impossiable to remove. She is a plant.
This was also why Duke's unit was chosen. CC wanted to take him out as payback, but when Duke joined up with GI Joe, it set up the whole scheme even better.