~Lets See so far~
Team Rocket (Leafgreen/Firered, Blue/Red/Yellow, Gold/Silver) - Trying to steal Pokemon from Trainers, the Leader created a Mewtwo from a Mew design. Took over Mt. Moon for some unknown reason?!? Captured an old dude in the Ghost tower. Took over A corp. building and set up an Illegal Gambling Pokemon game. Plus Cutting off Slowpokes tails in G/S! I can't remember G/S that much I think they did more!
Yeah, in Metalgen they were continuing on without their boss, they were suppossed to have disbanded but they took over Goldenrod Radio Tower to try to convey the message to their boss that they were still fighting on. They also caused a commotion at Lake of Rage. And in that city (can't remember which) with Price as the Gym Leader, they set up a secret hideout that you had to infiltrate. Yeah, they're pretty bad when you think about it, but I still say Cipher and Galaxy, they can really harm the people, Pokemon and world.