Wario Land 3
Rudy the Clown was an evil being that arrived on a once peaceful world and attempted to take it over but was sealed away with the aid of 5 magical music-boxes, however he used the last of his power to curse the inhabitants of that world into strange monsters as punishment, during the course of the game an unseen Rudy has Wario collect these 5 music boxes to free him only to instantly betray Wario once he is free - attempting to kill him as he saw no further use for Wario. However Wario defeated the evil clown and with Rudy defeated the world he had cursed returned to normal - as thanks the people of that world allowed Wario to keep all the treasure he had found which, in Wario's view, made it a very happy ending.
Dr. Mario 64
In this game, Rudy the Clown is significantly smaller than in Wario Land 3 and now lives in the Mushroom Kingdom, implying than he somehow escaped the music box. He develops a bad cold and needs Dr. Mario's mega-vitamins to heal himself, however, since he's evil, he assumes Dr. Mario would never come to him, so he has his minions steal the mega-vitamins instead. Dr. Mario and/or Wario (depending on who your playing as) chase his minions across the world and to his castle, where Rudy confronts them directly. After the player defeats Rudy, they heal his cold and he thanks them, and the character your not playing as eats the mega-vitamins and, for some strange reason, turns into ether Metal Mario or Vampire Wario, the true final boss.