The comic opens with a documentary about the origin of Judge Doom. The documentary mentions the original character cel used to create Doom. Eddie Valiant is given credit for ending Doom's reign of terror by dissolving him in a puddle of Dip, stated as 'A victim of his own evil creation', and putting a stop to his plans to erase Toontown and build a freeway where it would have once stood.
A weasel is shown watching the documentary which is Slimy. He goes with two other weasels one of them is Flasher and the other we call Ragtag to find the original cell of Doom. They manipulate some animators to bring Doom back to life. With time, Doom remembers everything that happened to him, and now wants revenge against both Eddie and Roger Rabbit for ruining his plans.
Meanwhile, Eddie is called by C.B. Maroon, the new executive of Maroon Cartoons, who announces they are reopening the studio, and pays Valiant $500 to run a search on the background of Roger. Eddie finds Roger's records clean as a whistle.
Meanwhile, Roger and Jessica Rabbit are enjoying life at home as much as possible, despite Roger's unemployment following the close of Maroon Cartoon Studios. Roger gets a call from Maroon Cartoons, saying they are reopening the studio, and that they want Roger to come work for them. Roger accepts the offer, and the next day, Roger meets Maroon, who starts Roger off with a very low-budget film (depicted in a Hanna-Barbera-esque style). Roger angrily objects to his part in the film, and is fired ("Get me that other rabbit with the tiger for a buddy!").
The next day, Roger finds dozens of scandalous, untrue headlines centered on himself. He turns to Eddie to find out why this is happening. Eddie first meets with Maroon, and questions him about firing Roger. Maroon reveals himself as Doom, tells his plan to ruin Roger's reputation and then kill him. He and the weasels knock Eddie out and lock him up in a storage locker, where he meets the real Maroon. Doom, as Maroon, puts Maroon Studios up for auction, and the studio will be officially sold at noon.
Meanwhile, Roger and Jessica are about to leave for Simi Valley, but first go to Eddie's office to say goodbye, only to find the office ransacked. Jessica finds indentations of the address Eddie wrote on the last piece of paper he used. Rushing to the address, they find and rescue Eddie and Maroon. They leave to save Maroon Studios. Eddie sprays him and his weasels with the Dip-filled gag squirt gun, and before dissolving, "Maroon" reveals himself to be Doom.
The real Maroon announces he is reopening Maroon Cartoon Studios, and will be providing all the toon employees with work, including Roger and Baby Herman with a line-up of new animated short films, starting with Tummy Trouble.