On the third/final floor, Bubsy will face off against Oinker P. Once completed, the player will have to go to a boss level before proceeding to the next floor. Each floor consists of five stages which each share its own seperate theme such as: Egypt, Space, Music, Aerial and Medieval. From the start of the game, you can choose from East Wing or West Wing which share different stages. In Bubsy II, the player is given the option to which stages that the Bubsy can transverse in.

A multiplayer mode was added as well, where a second player could control one of Bubsy's younger relatives. One new feature in the game was the ability to shoot a Nerf gun.

The game did feature a little more variety than its predecessor. 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'. Unlike the first game where playing through the stages is linear, in Bubsy 2 the player gets to choose stages. The game plays very similar to the prior game in the series, as a 2D sidescrolling platformer. Bubsy brings his nephew and his niece to the park, so it is up to him and his friend, Arnold the Armadillo, to stop the doctor and close the Amazatorium. Hamm, has created a theme park, the Amazatorium, that is stealing historical events. Rob Paulsen, who had previously voiced Bubsy in the tv pilot, reprises his role as him. Like the original, the Sega Genesis and Super Nintendo version are virtually identical, however, the Game Boy version is drastically different, with different level design and only black and white graphics, unless played on a Super Game Boy, which applied very basic coloring. However, a different new development team headed by designer Cyndi Kirkpatrick was responsible for making the game, without original designer Michael Berlyn's assistance. The sequel moved into full production after the first game was released and was a commercial success. Development for the game started as early as a few months prior to the release of the first Bubsy game, with team members coming up with three possible scenarios for the game, none of them involving the first game's antagonists 'The Woolies'.

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