The game plays very similar to the prior game in the series, as a 2D sidescrolling platformer. Unlike the first game where playing through the stages is linear, in Bubsy 2 the player gets to choose stages. The player must still maneuver Bubsy through the level through jumping and gliding, and Bubsy still collects objects, only now they're "orbs" instead of "yarnballs". The game did feature a little more variety than its predecessor. One new feature in the game was the ability to shoot a Nerf gun. A multiplayer mode was added as well, where a second player could control one of Bubsy's younger relatives. Bubsy can now take three hits before losing a life.
A new theme park is announced. Bubsy, Arnold, and Bubsy's younger twin relatives are excited. Fearing that the place might get too crowded, the twins decide that they break into the theme park on the eve of its opening day. The theme park, operated by a corrupt entrepreneur, features virtual worlds of certain themes.