Bowser made his first appearance in Phoenix Wright MUSHROOM Attorney, acting as the prosecutor facing Phoenix Wright. His appearance in court is marked with extreme rudeness, burning everything in the courtroom, and excessive Swearing. It is later revealed that he forced Waluigi to lie in his testimony, framing Luigi for the murder of Princess Daisy. After this is revealed, Bowser breathes fire on his desk, somehow causing it to explode and sending him god-knows-where. It is later discussed that Bowser may have been the true killer, but it is never said for certain.
Bowser next appears in Phoenix Wright Turnabout Portal, yet again as an antagonist. He teams up with Manfred von Karma, Satan, and Doctor Eggman to form the BESK (Bowser Eggman Satan Karma) team. He first appears after Phoenix Wright and his cohorts travel to Mario World only to find that von Karma had already been there for several hours and had teamed up with him. Later, along with the rest of the BESK team, he attacks the main cast in a giant robot, leading to an extraordinarily epic fight. At the last second, Manfred von Karma reveals himself to actually be Phoenix Wright in disguise and proceeds to punch Bowser in the face so hard that he actually gets knock out. He is later killed along with Eggman when Gumshoe blows up the robot with them in it. It is later revealed that, as a ghost, he got a job at an amusement park's haunted house.