The Animaniacs first begin the game by telling the player "welcome to our videogame", before arguing on the absurdity of how they can be in a videogame when they are cartoon characters, not videogame characters. The main story is that the Warner Brothers and Sister are attempting to try and be closer to their favourite movie stars. Yakko forms a plan: they can open up a shop to sell movie memorabilia - so they must obtain four items from different movie sets to set it up.

There are seven stages within the game. Each stage (except the starting one) has one object to obtain, which can only be obtained at the end after defeating the level's boss.

Like most videogames, the Animaniacs have health indicators and a number of lives. The lives can be increased by obtaining either 100 stars, or obtaining a small golden form of their faces. Their health is indicated by their faces on the top left of the screen. When they smile, they are healthy, but when they are looking either tired, unhappy, or weak, then they should find health soon (which is found in the forms of several forms of ice cream or sweets or other kinds of food).

The levels are timed, so it is unwise to stay and wander aimlessly in one area.