Mad Scienstein is an enemy in Wario Land 3. Wherever he appears, he tosses potions at Wario that make him invisible. It's notable that, after Rudy the Clown is defeated and most of the enemies are turned back in the normal people, Mad Scienstein isn't seen among them, indicating that he's really one of Rudy's minions.
He also appears in Dr. Mario 64, where he is, indeed, a minion of the game's main antagonist, Rudy. In the game, he steals Dr. Mario's Megavitamins, thereby causing Dr. Mario and Wario (who wants to steal them for himself) to chase after him throughout the whole game. In reality, he was just trying to give the Megavitamins to Rudy because he's sick. Depending on whose story the player follows, Mad Scienstein either gets beat up by Wario, or ends up stealing the Megavitamins again, causing Wario to continuously chase after him.