I don't remember it being that out there:
MM1: Doctor Wily is Doctor Light Assistant and re-programs all the Robot Master to be evil instead of useful workers
MM2: Doctor Wily creates his own Robot Masters (and reading between the lines anything he can get is hands on, ie a fan/zappo lighter, etc).
MM3: Wily says he is sorry, works with Dr. Light to create a peace keeping robot (Gamma) and needs crystals from various mining world.
MM4: A new Robot PHD creates 8 new Robot Masters to prove he is the best robot creator in the world.
MM5: Protoman goes rogue, has a new army and kidnaps Light.
MM6: Mr. X creates a tournament of for the best robots in the world and then steal and reprograms them.