In the Paper Mario series, Bowser is portrayed as a funny, dim witted character who usually is regarded as a minor threat by others, despite him being a major boss in many other Mario games. He actually was a major boss in Paper Mario, but was reduced to being a minor boss in Paper Mario: The Thousand-Year Door. In Super Paper Mario he becomes one of the playable Four Heroes, and is noted for his large attack power and lack of speed.
Bowser holding the Star Rod in Paper MarioIn Paper Mario, he steals the Star Rod in another attempt to capture Princess Peach. He uses it to raise her castle and become invincible. After he is defeated at the hands of Mario and the Star Spirits, Kammy Koopa makes him even more powerful. This time, even the Star Beam won't work, so Peach and Twink take out Kammy, and Twink helps Mario defeat Bowser.
Bowser is a minor boss in Paper Mario: The Thousand-Year Door, and is also a playable character at the end of some chapters, but only for short periods of time. He finds out about the Crystal Stars near the beginning of Chapter 2, and unsuccessfully tries to get them throughout the entire game. He finds you after a match in Glitz Pit, and challenges you. He ends up not getting any of the Crystal Stars, and you beat him again later in the Palace of Shadow.
In Super Paper Mario, he is forcibly married to Peach by Count Bleck, who creates the Chaos Heart from the marriage. You find him in chapter 3-1 as a boss. After you defeat him he becomes one of the Four Heroes. His attack is double whatever the rest of the team is and he can breath fire. His final battle is against O'Chunks.