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Roger Rabbit: The Resurrection of Doom is a comic sequel between the film Who Framed Roger Rabbit and the Roger Rabbit short film Tummy Trouble.

The comic starts with Roger and Jessica Rabbit watching a documentary in the movie theater about the origin of Judge Doom. Originally, Judge Doom was a toon named Baron von Rotten, who took up the role of playing the main antagonist in select Hollywood movies, until an unfortunate accident, resulting in von Rotten suffering a concussion, and upon awakening, believing he is a real villain. This is when von Rotten began his crime career, starting with robbing the First National Bank of Toon Town, and killing Theodore 'Teddy' Valient by dropping a piano on his head, and thereafter, using the money he stole to spread all over the town in order to buy the election for the Toon Town Judge, where he assumed the new name of Judge Doom. Tne documentary briefly mentions the original character cel used to create Doom. Eddie Valient 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 Toon Town and build a freeway where it once stood. Although Roger is outraged by the absence of his name from the documentary.

However, Roger and Jessica were not the only ones watching the documentary. A weasel was there as well, and using the knowledge he gained from watching the documentary, he goes with two other weasels to find the original cel of Doom in a dumpster, brings it to a painter's office for her to repaint Doom's colors, and then to an animation processing lab to bring Doom back to life. They are successful, and with time, Doom remembers everything that happened to him, and now wants revenge against Roger for ruining his plans.

Meanwhile, Eddie Valient is taking a break from his work, on account of work being slow around that time of year, and starts a new liking for jellybeans, as a means of breaking his drinking habits. He is called by C.B. Maroon, the new executive of Maroon Cartoons, and announces they are reopening the studio, and pays Valient $500 to run a search on the background of Roger Rabbit. Finding Roger's records clean as a whistle, Valient gives the report to Maroon, and earns his pay.

Meanwhile, Roger and Jessica are enjoying life at home as much as possible, despite Roger being unemployed following the shutdown of Maroon Cartoon Studios due to the death of R.K. Maroon, by Doom's bullets. Roger then gets a call from Maroon Cartoons, saying they are reopening the studio, and that they want Roger to come back and work for them. Immediately, Roger accepts the offer, and the next day, Roger meets C.B. Maroon, who starts Roger off with a very low-budget film where all he is supposed to do is turn his head and say his line. To Roger, this is not animation, especially since it needs the classic squash and stretch motion. Finding Roger cannot perform under a low budget, C.B. Maroon fires Roger.

The next day, Roger finds dozens of scandal headlines centered on Roger (with the exception of moving to Simi Valley to open a restaurant there). He turns to Valient to find out why this is happening. Having formed a friendship with Roger, Valient takes the case, and first looks at the headline about a missing drum of paint thinner (aka Dip), Valient follows an address to a place where they store studio goods, but before he does, he meets with C.B. Maroon, and questions him on why he fired Roger. It turns out it is Doom in the guise of C.B. Maroon, who intends to ruin Roger's reputation, and only when Roger begs for the misery to end, will he kill him. He and his weasels knock Valient out and lock him up in a storage locker, where Valient meets the real C.B. Maroon, who was also locked away for identity purposes.

Doom, once again in the guise of C.B. Maroon, is now putting Maroon Studios on sale at an auction, and when a deal is made, the studio will be officially sold at noon. This also erupts angry protests by toons against the sale of the studio.

Meanwhile, Roger and Jessica are about to leave for Simi Valley, and on the way, go to Valient's office to say goodbye, only to find the office having been trashed. Thanks to Jessica's brilliant eye sight, they find indentations of the address Valient wrote on the last piece of paper her used, and rush to the location, and find Eddie Valient inside, who was about to spray him with a squirt gun full of dip, from the missing drum of paint thinner having been kept in that same storage locker. There, Roger also meets C.B. Maroon. Outraged, but unaware of that being the real C.B. Maroon, Roger attacks him, but Valient calms him down, and explains the situation. They leave for Maroon studios. Though they arrive after the noon deadline, Valient knows Doom is impersonating Maroon, and sprays him and his weasels with the Dip-filled gag squirt gun, and before they dissolve and melt away into the sewers of the streets, Doom reveals his real identity.

The real C.B. Maroon announces he is reopening Maroon Cartoon Studios, and will be providing all the toon employees with work, including Roger Rabbit and Baby Herman with a line-up of new animated short films, starting with Tummy Trouble.