Cobra's plan was totally worthy of the old cartoons, I guess, in that they go to ludicrous amounts of effort in order to accomplish something trivial. I guess it would be a spoiler to say what...
They spend billions developing nanotech warheads for NATO in order to steal them back (this takes them a few tries), travel to France to activate them, and then to the North Pole to load them onto intercontinental ballistic missiles (instead of, say, carrying the tiny devices into the cities they were planning to attack) aimed at Moscow, Beijing, and Washington.
Why? So that they can trick the president of the united states into going into his underground bomb shelter. THAT WAS THE WHOLE POINT. Gaaah!
Oh, and apparently everyone in GI-Joe and Cobra know each other from way back. I lost track of how many people were the Baroness' ex-lovers.