Bowser Jr. first appeared in Super Mario Sunshine, where he helped his father take over Isle Delfino and cover it with filth. He did this with a magic paintbrush that allowed him to create a foul substance called "Goop", as well as to take on the form of a shadowy duplicate of Mario. After being defeated at Isle Delfino, Bowser Jr. would go on to assist his father in other plans, taking over a role once held by his siblings the Koopalings. However, all of Bowser's known children worked together to help their father take over the Mushroom Kingdom in New Super Mario Bros. Wii.
Bowser Jr. first appeared as a background character in 190 - Where's Waluigi?, but his first (and currently only) major appearance was during the A Mushroom Kingdom Carol story arc. At some point in the future, Bowser would be defeated for good by the Mario Bros., leading the Mushroom Kingdom into an age of prosperity. However, years later, Bowser Jr. would grow up and take over again, with Mario too old to stop him. After receiving an epiphany in the form of the Spirits of Christmas, Mario regained his old heroic ways and was able to defeat Jr. by spraying him with F.L.U.D.D. until the pair reached one of Bowser Castle's rickety wooden bridges, which Mario was able to sever, plunging Jr. into the lava like his father many years before.