First one isn't same continuity as second, although a fic where Team Rocket starts brainwashing trainers would be a great idea.

Second one is AU Legend of Thunder, working off the theory that the events of the movie were a dream while Marina was put out and in reality she's a captive of Team Rocket.

Yeah, Sebastian gave Marina a serum that pretty much brainwashed her into compliance with any orders given him. He's a sick fuck so of course he tells her to kill her friends.

Yeah, take the icon! I made it years ago, it's a quote from The Office.