Those lab mice bent on world domination, Pinky and The Brain, have hatched a new scheme to try to take over the world! Their latest plan is to steal a prized script from Warner Bros. Studios, which they will produce to earn them enough money to take over the world. The CEO of Warner Bros. asks Yakko, Wakko and Dot to recover all 24 scenes of the film's script.
Animaniacs is a platform game where you control the three Animaniacs, Yakko, Wakko and Dot. Players can cycle between their current Animaniac by using R Button, and in addition to jumping, the player can stack the Animaniacs on top of each other to reach places they couldn't on their own. The Animaniacs can pick up and throw small objects to attack, as well as dash to break objects and dodge enemies. Larger objects can be pushed, to access higher areas, or sometimes to reveal secrets.
If a Warner is captured by Ralph, Warner Bros.' security guard (which is equivalent to "death"), the player has a chance to rescue all the Warners lost by entering the Water Tower stage from the map. After negotiating this small stage and reaching the top of the tower, it opens and all the Warners are rescued.
Script scenes are key to finishing the game completely. A few are given to players for finishing the level, but others are hidden in secret places and players must perform special tasks to locate them all. The other collectable aside from script scenes are coins. These coins are used to start a slot machine that is at the bottom of the screen. Depending on the way the reels land, players may get an extra continue, invincibility, all of the Warners returned, more coins, or lose some of their coins.