Roger Rabbit's, a living breathing cartoon, has been framed for the murder of Marvin Acme. The motive is that his wife, Jessica Rabbit had been photographed playing patty-cake with him. Obviously this kind of affair is enough to drive a man, or rabbit, into killing. But he didn't do it and now there seems to be some kind of mystery surrounding Marvin Acme's last will and testament... and with it, ownership of Toontown. In order to clear his name, Roger has enlisted the help of Eddie Valliant, no-nonsense detective. Together they'll need to search through Hollywood, Toontown, the Wilderness and Toontown in an effort to find the pieces to Marvin's original will and stop the evil Judge Doom and his henchmen, the Weasels.

You play this game as the Private Investigator, Eddie Valliant, while Roger Rabbit wanders around the scenery behind you. Your job is to search the city for clues, items and punchlines to jokes which will be your only defense should the Weasels catch up to poor Roger. Except for these Weasels (and birds flying overhead), Roger is more or less invincible as a toon. That means for most of the gameplay, he will be ignored. Should the Weasels appear in an area with you however (with an alarm sounding as they get close), Roger will go bug-eyed and try to run away. It is then up to Eddie to keep the Weasels away from Roger or engage in knock-knock jokes should they happen to catch him.

The bulk of the gameplay takes place on side-scrolling areas that represent city blocks, caves and room interiors. There is also a top-view world map where you navigate between areas on foot or via Benny the Cab.