Players control Yakko, Wakko, and Dot, switching control between them to use their respective powers accordingly. After clearing all five levels, players travel to the final level where they must fight Pinky and the Brain. A fifth level will then open to obtain a final piece of movie memorabilia. The player must reach the end of each level and beat the boss to obtain a piece of movie memorabilia. The game features four main levels, which can be entered in any order. being able to complete the film, pleasing the CEO, only to find out that the film was about the Warner Siblings, which pleases them. The ending of the game depends on how many script pages are collected, with the best ending leading to Warner Bros. studio reluctantly asks the Warner Siblings for their assistance to retrieve all 24 pages of the script and foil the Brain's plan, which is the primary objective of the game.

In the SNES version, the Brain once again has another plan to conquer the world by deciding to steal the script of the new Warner Bros. However, once they collect all the memorabilia, Pinky and the Brain attempt to steal them in order to further their world domination plans. studio lot in order to retrieve movie memorabilia to sell. To this end, they travel across various movie sets in the Warner Bros. In the Genesis version, the Warner Siblings, Yakko, Wakko, and Dot, decide to open up a hip-pop culture shop in order to become closer to their favorite movie stars.

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