If I remember correctly, I'd have maybe 60 or 70 Operatives on stand-by in the late-game, but I know it was way more in my last win. I just love being able to work with different teams world-wide, especially renaming them as a whole and I'm a big g.i. Joe fan, so Cobra Vipers go! Then next I can send out my Alley Vipers, or The Dreadnoks if the price is right. My Snow Serpents will be stationed in the North and South Poles. Then out of my Cobra Legions world wide, I will pick out the best of the best to form the Crimson Guard to protect the new Cobra Commander when he decides to personally deal with the Aliens and for the final mission. The Crimson Guardsmen will be equipped with the best of the best armaments.
Of course, other members of the Cobra Hierarchy will be commanding the other bases.
If the Commander goes down in a battle, I'll give him one more chance, since he has been able to recover from near death in his comics thanks to his loyal agents. After a second death, next up will be Destro, then the Baroness with burning revenge, and then the twins, Tomax and Xamot. Serpantor, maybe.