The movie is set in 1957, ten years after the original.
Opening cartoon
The movie begins as the first film does, with a cartoon short. It is called, "Roger Rabbit Goes To the Dogs". It is in Cinemascope, as if hinting that Maroon is also trying to lure audiences back into theaters as other studios do, using such gimmicks as Cinemascope, 3D and stereophonic sound.
We fade in on a curtain, which opens, as the Maroon Cartoons theme music plays. What follows is a new title sequence for the cartoon, as it is in Cinemascope, as is the rest of the movie. It's the same music as before, but visually, the sequence is very different. It looks like the title sequence for the Disney Cinemascope cartoons of the period. But in this case, Donald Duck holding the flashlight is replaced by Roger Rabbit, and the image in the light is of the usual heads of Roger and Baby Herman, but in this case, Baby Herman's head is more hidden behind Roger, as if peeking out from behind the rabbit. Then we fade to another shot of the stylized Roger shining the light on numerous titles around him. In the upper left corner, it reads, "R.K. Maroon, Jr. presents"; in the lower right corner, it reads, "A Maroon Cartoon"; in the lower left corner, it reads, "In Color"; and in the upper right corner, it reads, "Copyright MCMLVII By the Maroon Corp. All Rights Reserved". Then, clock-wipe to another title shot, this one displaying Roger and Herman, with the words, "Roger Rabbit and Baby Herman", and then iris in to black, then iris back out to one last title, this time displaying the words, "in 'Roger Rabbit Goes To the Dogs', Directed by Mel Turner", along with the MPAA logo underneath. Underneath the title are silhouettes of Roger and Herman, along with those of a dog wearing a hat and a dogcatcher. Roger is trying to sneak up behind the baby who is reaching out playfully to the dog, while the dogcatcher is trying to sneak up behind the dog, his net at the ready. Then we fade out and the cartoon begins...
A dog, looking like the one in the title card just a second before, is seen walking down the street on his hind legs. He wears a hat on his head and humming the Maroon Cartoons theme. This dog is the one we later identify as Norty, whose personality is based on Art Carney's character Ed Norton from "The Honeymooners" and is also a homage to characters voiced by Daws Butler, which the dog is also supposed to sound like. This cartoon's opening resembles the opening for the MGM cartoon "Give and Tyke". Norty walks down the street and hums the Maroon Cartoons theme, minding his own business. He walks off the street and into an alley. He sees two trashcans.
Norty sniffs around the trashcans and looks through them. Like a slot machine, several images roll in circles in his eyes, eventually landing on a T-bone steak and making a "caching" sound. Norty dives into the cans and creates quite a mess. The can eventually falls over and he falls out with a bucket on his head. Yanking it off, he picks up a chicken leg and begins to eat it, picking up a nearby newspaper. He then walks off, humming again, to find someplace to sit down and eat. As he sits down on a crate to eat, he then holds up the newspaper to read it. But suddenly, he is shocked by what the headline reads: "LAST DAY FOR FREEDOM OF UNLICENSED DOGS!" Underneath it, it reads, "All unlicensed and/or homeless dogs will hereby be locked up in the city pound." As he reads the paper, Norty drops the drumstick in shock and imagines himself at the pound, which resembles a jail cell, dressed like a convict (all black and white stripes) and playing "Nobody Knows the Trouble I've Seen" on a harmonica. He looks over his shoulder, and whom should he see but a dogcatcher who discovers Norty and advances on him, his dark shadow cast over the dog.
Norty screams and jumps into the air, his very ghost emerging from his body, also screaming. Norty runs away just as the dogcatcher swipes at him with a net. His ghost, on the other hand, just misses it and speeds after Norty, Norty gesturing for him to return to his body in which he does. The dogcatcher follows in hot pursuit. The dog manages to slow down the dogcatcher by knocking over a stack of trashcans in his path. The dogcatcher stumbles and trips over the trashcans. Meanwhile, Norty runs out of the alley and around a street corner. The dogcatcher follows, huffing and puffing. The dogcatcher chases him for a few seconds as the background is seemingly looped over and over again. The dogcatcher closes in on his prey, but Norty finally leaps away, leaving a cloud of dust in the dogcatcher's path. The dogcatcher runs into the dust and starts coughing. Meanwhile, Norty runs up to another corner in a suburban area. He frantically looks around for a place to hide, his legs and feet dancing furiously. Suddenly, he discovers that he is standing next to a white picket fence surrounding a house. He looks at the mailbox by the gate, which reads, "The Hermans". He then looks toward the house's window, which shows a silhouette of a woman pointing her finger at a silhouette of a rabbit. Suddenly ecstatic, Norty digs a hole in the grass at the base of the fence, to the sound of a jackhammer in the background, and then burrows into the hole like a gopher. He burrows under the fence and into the yard toward the house. We cut inside the house, which is the usual house of other Roger Rabbit cartoons.
Inside, Mrs. Herman is pointing her finger at a nervous-looking Roger Rabbit. Behind them, in the playpen, is Baby Herman. He looks like he is on the verge of tears. Mrs. Herman is soundly berating Roger for his tomfoolery (or possible lack thereof). She tells Roger that she is tired of his conduct and that he is worth more trouble than he is worth as a rabbit. Roger begs for another chance. Reluctantly, Mrs. Herman agrees. Roger is ecstatic, shaking her hand and telling her she won't regret and that he'll be the best babysitter she ever had, even turning to Baby Herman for support, who giggles and makes a flatulence sound with his tongue. Roger gulps. Mrs. Herman tells them that she is going to the morgue. She tells Baby Herman to be a good kid for Roger and then warns Roger not to slip up anymore or to let any strangers in the house or he will be sent to a rabbit furrier. Roger gulps. Mrs. Herman starts while Roger reassures everyone that he won't be going to the furrier and rambles on that he is "a master of babysitting", a pillar of virtue", etc., while Mrs. Herman ignores him and leaves, her footsteps receding as she goes through the door and closes it with a slam.
As Roger continues to ramble on, he never notices the baby getting out of the playpen by squeezing through its bars, which he does with ease. Baby Herman then crawls over to the nearby window, which is open. He sees Norty staring at him through it and licking his face. As he finishes his spiel, Roger turns confidently to his charge, only to notice that the playpen is empty. He looks around and sees Herman being licked by Norty through the window. Roger smiles at the dog being on the property. Then after a beat, he does a classic double take and becomes alarmed at the dog being on their property. He goes crazy as usual (eyes bugging out, to the usual sound effects, and screaming) and runs at Baby Herman, shouting that he is too little to play with dogs.
The rabbit snatches up the baby and pulls him away from Norty's clutches. Unfortunately for him, Roger doesn't look where he is going. He slams into a wall and drops Herman who immediately crawls back over to Norty. A flattened Roger (with missing teeth) gets up and calls to Baby Herman once more, but to no avail. The rabbit notices a book standing in a diagonal position on a nearby bookshelf. It reads: "DOGS – Man's Best Friend or Man's Worst Enemy". Roger takes the book and opens it. He then reads a selection out loud: "How to train your dog. Step one: Butter him up with kindness." Dashing into the kitchen, Roger opens up the fridge and takes out a slab of butter. He then approaches Norty, who is still licking Baby Herman, and pokes his shoulder to get his attention. When the dog turns to face Roger, he smashes the butter all over Norty's face, having literally buttered him up. Roger gives the dog's head a gentle pat. Norty, however, becomes angry and growls at Roger, baring his huge teeth at him.
Norty attacks Roger and the two get into a big fight (which, as is the case with most cartoons, is mainly obscured by a huge cloud of dust that obscures everything), much to Roger's dismay and Baby Herman's amusement. Roger jumps out of the cloud of dust and snatches up the book. He flips through the pages of the book again, eventually landing on a page. It says, "Step two: Discipline the dog." However, Roger being Roger, he misread "discipline", thinking it is "disintegrate". He shrugs and goes to a hallway, where he sets a timer for a large set of TNT (with the ACME label on it, obviously) nearby. Poking his head out, he sees Norty trotting towards him. "Boy, that Acme, what a genius!" Roger muses, foolishly acting casual. He leans his hand on the wall, with the timer behind his back. Norty approaches him and again growls at him, advancing on him slowly. Roger presses the timer rapidly. Nothing happens. He presses it again. Still nothing. Roger is puzzled, unable to figure out what went wrong. Norty continues his advance on Roger. Still, Roger continues to press the timer repeatedly, until finally, the TNT explodes. This causes a mushroom cloud explosion to emerge from the house. Inside, everything is unharmed except for Roger who is merely a pile of ash with eyeballs.
Wipe to a later scene. A greatly-damaged Roger watches Baby Herman and Norty at play. He is very sad. He carries a suitcase with him, knowing that he's going to the rabbit furrier. "Well, I tried," he says sadly. He takes a look around and sees the mess that they made. A broken window, charred walls and a massive hole in the ceiling (even though the house appeared unharmed at first), the mess made near the fridge, and butter splattered and stained onto the floor. A tear forms in Roger's eye and his sniffs. Just then Mrs. Herman returns and bursts through the door. She announces her arrival home and then screams. She shouts at Baby Herman – not Roger – for letting a dog in the house and that she is allergic to dogs. Suddenly, she lets out a sneeze so huge that everyone is blown back a bit. She orders Baby Herman to his room. Herman looks shocked, then suddenly, he darkens. Anger starts building inside him. Meanwhile, Roger approaches Mrs. Herman with his luggage, hanging his head.
He puts out his hand in friendship to Mrs. Herman, saying that it's been nice knowing her, but to his surprise, she picks him up and kisses him all over, asking for forgiveness for misjudging him all these years. She then puts him down. He is covered in red lipstick marks. Roger looks puzzled, but then gets ecstatic. But no sooner does he agree to this, than suddenly an angry Baby Herman yells, in a gravelly adult voice, "Cut!"
Segue into live action
The camera pulls back to reveal that, as in the first movie, this movie's cartoon is shot live on a live-action movie set. Only the Toons, Roger, Baby Herman and Norty, are still Toons. From the equipment and the dress of the crew, we can tell it's the 1950s. Norty exclaims, "Hey! What the hell's wrong with that take?" Herman tells him that it's supposed to be his cartoon and that he and he alone is allowed to win. He demands to know who wrote the script. Mel Turner, the director, walks up.
MEL: Can I offer you a cigar, Mr. Herman? Or maybe a clean diaper? Anything to help you get back to doing things here? Here we are, trying to make an impression on our new boss, R.K. Maroon, Jr., our founder's son, and we're already behind schedule and overbudget! We must get back on! I thought you heard all about Roger's newest fame in this series. You did hear, didn't you?
Baby Herman looks up at Mel with a scowl.
BABY HERMAN: (growling) How dare you, chump! I've been the star of these cartoons since before you picked up a megaphone! I NEVER LOSE!
Mel rubs the perspiration off his forehead. He then picks up his coat.
MEL: I can't take this anymore, I quit!
Baby Herman jumps up on Mel's coat sleeve, this time with a pleading look on his face.
BABY HERMAN: Please, Mel, I beg of you. Why make Roger the star? He's nothing but a buck-toothed wise guy! I'm the cute one, the Bambi of Maroon Cartoons!
Baby Herman gets dragged off-camera on Mel's shoulder. Carol Masters, a female photographer, watches them leave and turns toward Roger.
CAROL: Well, Roger, how does it feel to be in the leading role for once? Pretty good, huh?
ROGER: You bet, Carol!
CAROL: You do realize, though, that Baby Herman is not very happy with you, right?
ROGER: Aw, who needs him? It's nice to be out from under his shadow.
Roger and Norty turn to leave. They exit from the soundstage and out onto the Maroon Cartoons lot, to a large group of paparazzi reporters.
ROGER: (blowing kisses to the crowd) Thank you, thank you, I love you, I love you. P-p-p-p-lease, no pictures. I'm having a bad ear day.
Norty happily slaps Roger on the back.
NORTY: I tell ya, Rogey boy, ever since you became the logo for Maroon Cartoons things have really been goin' swell for us Toons, eh?
The two walk across the backlot of Maroon Studios. They look up to stare at a large water tower with Roger's face on it and the studio name underneath him.
ROGER: Jeepers, it sure does feel nice, doesn't it? No longer being a comic foil to become a leading role. That sure is swell, eh, Norty? Why, one of these days, I just might make you as big a star as I am, pal.
NORTY: (laughs) Yeah, right. As much as I wish that'd happen there, Rog, I bet that in a year or two, I'll probably have a better chance of being R.K. Jr.'s personal paperboy!
Roger and Norty continue along the backlot and eventually reach the main offices of Maroon Studios where R.K., Jr.'s office is.