The gameplay involves navigating through various environments, such as a ship, harbor, streets of Manhattan, sewers, and a pier, to collect cheese or avoid obstacles. The player controls Fievel or other characters, using rolling, flying, or skating abilities to overcome challenges. Stars can be collected as additional challenges, with some levels featuring vertical gameplay.
The game features different control schemes for each level, requiring the player to adapt to new situations and environments. The levels are designed to evoke scenes from the movie, with animated cut-scenes used throughout.