The story is a murder mystery set in 1947, in a surreal world where cartoon characters, commonly called "Toons", are living beings who act out cartoons in the same way that human actors make live action productions. Toons interact freely with humans and live in an area near Hollywood called Toontown. R. K. Maroon is the human owner of Maroon Cartoon studios; Roger Rabbit is a fun-loving Toon rabbit, one of Maroon's stars; Roger's wife Jessica is a gorgeous Toon woman; and Baby Herman is Roger's costar, a 50-year-old Toon who looks like an infant. Marvin Acme is the prank-loving owner of Toontown and the Acme Corporation.
The trouble begins when Maroon hires privavite detective Eddie Valiant to investigate rumors that Jessica is having an affair. Eddie and his brother Teddy used to be friends of the Toon community, but Eddie has hated them, and has been drinking heavily, since his brother Teddy was killed by a Toon a few years earlier. Before heading to the club where Jessica, Eddie visit the bar where his girlfriend Dolores works at; She tell himthe his nephew Sora has come to visit and her niece and nephew have came to wit thier friends, he takes them to the Ink and Paint Club; Where they see Donald and Daffy having a piano duel & met Marvin. Later, on Eddie goes take the photos of Jessica after being thrown out of the club. When he shows Roger photographs of Jessica "cheating" on him by playing patty-cake with Acme, Roger becomes distraught and runs away. This makes him the main suspect when Acme is found murdered the next day. At the crime scene, Eddie meets Judge Doom and his Toon Patrol of weasel henchmen. Although Toons are impervious to physical abuse, Doom has discovered that they can be killed by dissolving in a mixture of paint thinners he calls "The Dip".
Baby Herman insists (correctly) that Acme's will, which is missing, bequeaths Toontown to the Toons. If the will is not found by midnight, Toontown will be sold to Cloverleaf Industries, which recently bought the Red Car trolley line, a local transportation provider. After noticing the will in one of the patty-cake photographs, and after Roger shows up at his office protesting his innocence, Eddie investigates the case with help from his girlfriend Dolores while hiding Roger from the Toon Patrol. Jessica tells Eddie that Maroon blackmailed her into compromising Acme, and Eddie learns that Maroon is selling his studio to Cloverleaf. Maroon explains to Eddie that Cloverleaf will not buy his studio unless they can also buy Acme's gag-making factory. His plan was to use the photos to blackmail Acme into selling. Before he can say more, he is shot dead by an unseen assassin and Eddie sees Jessica fleeing the scene. Believing she is the killer, Eddie pursues her into Toontown. When he finds her, she explains that Doom killed Maroon and Acme in an attempt to take over Toontown.
Eddie, Jessica, and Roger are captured by Doom and his weasels and held at the Acme Factory, where Doom reveals his plan: Since he owns Cloverleaf and Acme's will has yet to turn up, he will take control of Toontown and destroy it to make room for a freeway, then force people to use it by dismantling the trolley fleet. He has also built a mobile Dip sprayer with which he intends to wipe out the Toon population.
With Roger and Jessica tied up, Eddie performs a vaudeville act that makes the weasels literally die of laughter. In the climactic struggle between Eddie and Doom, Doom is revealed to be a Toon and admits that he killed Teddy, and Eddie dissolves Doom in Dip by opening the drain on the Dip machine. As Toons and the police arrive, Eddie discovers that an apparently blank piece of paper on which Roger wrote a love poem to Jessica is actually Acme's will written in disappearing/reappearing ink. Eddie gives Roger a big kiss, and the Toons celebrate their victory.
- Guest Starring: Sora
- It was planned to Featured The Icarly gang, but was trapped due to copyright issues; Bonkers appearance was also dropped due that the movie "Sonic The Hedgehog Meets Bonkers" was dropped
- Eggman is not in this film
- Famly members introduce
- Sora is Dolores' nephew