The SNES videogame of Animaniacs is more complex and challenging than its 16-bit counterpart on the Sega Genesis. This game is out of the ordinary because movement is forwards, backwards, and side to side (all levels have paths that move the characters on three lanes to avoid enemies and obstacles), whereas in most 2D platform games the player can only go forward and back. Pinky and the Brain once again have another plan to conquer the world by deciding to steal the script of the Greatest Movie ever while it was under development (this is not any actual movie or parody of one). The CEO of Warner Brothers studio reluctantly asks the Animaniacs for their assistance to retrieve all 24 pages of the script, which is the primary objective of the game. This game can be completed without obtaining all of them, however. The game focuses more on parodies of films at the different stages that are once more based on different genres of movies.

This game is more complex for two reasons. Firstly, the characters have no health bar, lives (the game ends when all the characters are defeated/captured, one by one) or special abilities. Secondly, there is the slot system, which is a slot machine at the bottom of the screen. It activated after obtaining a certain number of coins and can be used for a range of power ups such as temporary invincibility or bringing back characters who were defeated or captured earlier.

Throughout the game, there are small creatures with white block heads, red bodies and yellow appendages. The purpose they have in the game is unknown.

The levels listed below can be completed in any order. Rather than explain the level structure, parodies will be listed: