In 1947, "toons" act out theatrical cartoon shorts as with live-action films; they regularly interact with real people and animals and reside in Toontown, an animated portion of Los Angeles. Private detective Eddie Valiant and his brother, Teddy, once worked closely with the toons on several famous cases, but after Teddy was killed by a toon, Eddie lapsed into alcoholism and vowed never to work for toons again. One day, R.K. Maroon, head of Maroon Cartoon Studios, is concerned about the recent poor acting performances of one of his biggest stars, Roger Rabbit. Maroon hires Valiant to investigate rumors about Roger's voluptuous toon wife Jessica being romantically involved with businessman and gadgets inventor, Marvin Acme, owner of both Acme Corporation and Toontown. After watching Jessica perform at the underground Ink & Paint Club, Valiant secretly takes photographs of her and Acme playing patty-cake in her dressing room, which he shows to Roger. Maroon suggests to Roger that he should leave Jessica, but a drunken Roger refuses and flees.
The next morning, Acme is discovered dead at his factory with a safe dropped on his head, and evidence points to Roger being responsible. While investigating, Valiant meets Judge Doom, Toontown's Superior Court judge, who has created a substance capable of killing a toon: a toxic chemical known as "The Dip". Valiant runs into Roger's toon co-star, Baby Herman, who believes Roger is innocent and that Acme's missing will, which will give the toons ownership of Toontown, may be the key to his murder. He then finds Roger hiding in his office, who begs him to help exonerate him. Valiant reluctantly hides Roger in a local bar where his ex-girlfriend, Dolores, works. Later, Jessica approaches Valiant and says that Maroon had forced her to pose for the photographs so that he could blackmail Acme.
Doom and his toon-weasel henchmen discover Roger, but he and Valiant escape with Benny, an anthropomorphic toon cab. They flee to a theater, where Valiant tells Roger about Teddy's death. As they leave with Dolores, Valiant sees a newsreel detailing the sale of Maroon Cartoons to Cloverleaf, a mysterious corporation that bought the city's trolley network shortly before Acme's murder. Valiant goes to the studio to confront Maroon, leaving Roger to guard outside, but Jessica knocks him out and puts him in the trunk. Maroon tells Valiant that he blackmailed Acme into selling his company so that he could then sell the studio, but is shot dead before he can explain the consequences of the missing will. Valiant spots Jessica fleeing the scene and, assuming she is the culprit, follows her into Toontown. Jessica reveals that Doom killed Acme and Maroon, and that the former had given her his will for safe-keeping, but she discovered that the will was blank. She and Valiant are then captured by Doom and the weasels.
At the Acme factory, Doom reveals his plot to destroy Toontown with a giant machine loaded with Dip to build a freeway, the only way past Toontown since Cloverleaf (which Doom owns) has bought out Los Angeles' tram system. Roger unsuccessfully attempts to save Jessica, and the couple is tied onto a hook in front of the machine's hose. Valiant then performs a comedic vaudeville act, causing the weasels to die of laughter; Valiant kicks their leader, Smart Ass, into the machine's Dip vat. Valiant then fights Doom, who is eventually flattened by a steamroller, but survives. Eddie is shocked when Doom reveals that he is a toon in disguise the same toon who killed Teddy. Valiant uses a toon mallet with a spring-loaded boxing glove, and fires it at a switch that causes the machine to empty its Dip onto Doom, killing him. The empty machine crashes through the wall into Toontown, where it is destroyed by a train. Numerous toons run in to regard Doom's remains, and Roger discovers that he inadvertently wrote his love letter for Jessica on Acme's will, which was written in disappearing-reappearing ink. Roger then shocks Valiant with a joy buzzer, and Valiant gives him a kiss, having regained his sense of humor. Valiant happily enters Toontown with Dolores, and Roger with Jessica, followed by the other toons.
Output: How does Eddie kill Doom's weasels?