Bowser has appeared in all three of the Mario & Luigi games.
In Superstar Saga, he attempts to kidnap Princess Peach after her voice is replaced with a literal explosive vocabulary by Cackletta. After a battle with Mario, he helps him to try and recover Peach's voice. On the way to Beanbean Kingdom, they are attacked by Fawful and after some events, Bowser ends up with amnesia. While under the effects of amnesia, he ends up grouping with Popple under the alias of Rookie. In the end, he is possessed by Cackletta and becomes Bowletta, only to return to normal after being defeated by Mario and Luigi.
Partners in Time has Bowser appearing as a minor villain. He actually meets with the infant version of himself, Baby Bowser, even teaming up with him to fight the Marios and Luigis. He is later inhabited by the spirit of Elder Princess Shroob, forming Shrowser. After the final battle, Shrowser is defeated and free of being possessed, ending up unconscious.
In Bowser's Inside Story, he is once again playable and is considered the main protagonist. After getting kicked out of the meeting at the beginning, he ends up getting an item called a "Lucky Mushroom," which was really a Vacuum Mushroom that allows Fawful to control Bowser. This mushroom granted him the ability to inhale everything, which Fawful uses to inhale everyone at the conference.
