Bass and the Robot masters are not advanced enough to make their own decisions. Zero was made with strong power, but as a result, also had free will. Wily put a virus in Zero to control him, and sealed him in a capsule, possibly to let the virus take effect. 100 years later, Zero fights Sigma(Who is a Maverick hunter at this point). Zero\'s free will fights the virus and he goes insane. Zero loses due to a error in his programming. The virus enters Sigma, turning him Maverick. Zero recieves free will.