As a young boy of 8, Plucky Duck falls down a well, where he is caught in a swarm of bats. Plucky is rescued by his father, but he is left with a fear of bats. When Plucky and his parents attend "What's Opera, Doc?", but Plucky is frightened by some bats flying through the old theater. He and his parents exit into an alley, where they are confronted by an armed mugger, who shoots and kills Plucky's parents. He is arrested and convicted for the double murder, but Plucky is left traumatized by the incident. The family's butler, Daffy Duck, raises Plucky in the absence of his parents.
When Plucky becomes a young man, he returns home to ACME Acres from Princeton University, intended to kill the murderer of his parents, whose prison sentence is being suspended in exchange for testifying against the mob boss Montana Max. The assassin is assassinated by one of Monty's henchmen, depriving Plucky of his opportunity. When Plucky tells his childhood friend Shirley The Loon about his foiled plan, she expresses disgust and gives him a lecture about the difference between justice and revenge. Realizing she is right, Plucky decides to confront Monty himself, but the mob boss dismisses him as ignorant of nature of the underworld ("You're Plucky Duck, the Prince of ACME Acres, you'd have to go a thousand miles to find someone who doesn't know your name!"), having his thugs rough him up. Realizing that Monty is right, and that he cannot truly understand what he intends to fight as a wealthy playboy, he abandons his life at home, stowing away on a cargo ship and traveling the world for nearly seven years.
Plucky associates with three criminals he met to learn their ways and is thrown in prison by police in California for theft, ironically, property of his own company, Duck Enterprises. After a prison brawl, an enigmatic woman who identifies himself as Rhubella invites Plucky to join an elite vigilante group, Perfecto Prep, under the leadership of Roderick Rat. Plucky is freed the next day and travels to the top of a mountain to begin his combat training with the group. In his training, Plucky overcomes his fear of bats while under the hallucinogenic influence of a mountainside blue flower. Following his training, Plucky will be accepted in Perfecto Prep and help them in their fight to restore order to ACME Acres. When Rhubella orders Plucky to execute a murderer as a final test, Plucky refuses to obey and destroys Perfecto Prep, accidentally killing Roderickin the process. However, Plucky rescues an unconscious Rhubella from the wreckage and leaves his mentor at a nearby village.
20 years after Plucky's parents' death, Plucky Duck returns to a ACME Acres that is mostly ruled by Montana Max and begins plotting a one-man war against the corrupt system. He seeks the help of Shirley, now an assistant district attorney, and police sergeant Buster Bunny, who consoled him in the aftermath of his parents' murder. Plucky pays a visit to Buster one night in disguise to establish communication. After reestablishing his connections to his father's company, Duck Enterprises, Plucky is able to acquire, with the help of former board member Calamity Coyote, a prototype armored car and an experimental armored suit. He augments the suit with Perfecto Prep armor, and a special cape that can become a rudimentary hang glider.
One night, in his new "Batduck" costume, he disrupts a drug shipment by Monty, and leaves the mob boss tied to a searchlight, forming a makeshift Bat-Signal ("I'm Batduck"). He also disrupts an assassination attempt on Dawes, leaving her with evidence against a judge that has gone soft on Monty in the past. While investigating the "unusual" drugs in the shipment, Batduck is stunned by Mary Melody ("The Scarecrow"), who sprays him with a powerful hallucinogen. Plucky is rescued by Daffy, administered an anti-toxin developed by Calamity and awakens two days later on his thirtieth birthday. Melody later, in her asylum, ACME Looniversity, poisons Shirley after showing her that the toxin, which is revealed to only be harmful in vapor form, is being piped into ACME Acre's water supply. She is saved by Batduck. The police enter the Looniversity, and Batduck escapes with Shirley in his Batmobile. After administering the antidote to Shirley in his cave, he gives her two vials of it for Buster; one for the detective to inoculate himself, and another to mass-produce for the population.
Later at a party held at his mansion, Plucky is confronted by a group of ninjas from the Perfecto Prep and his old mentor Rhubella, who had been conspiring with Mary the entire time, plans to destroy ACME Acres by distributing the toxin (which was extracted from his blue flowers) undetected via ACME Acre's water supply, and then vaporize it with a microwave emitter stolen from Duck Enterprises. Plucky, tricking his guests into leaving, fights briefly with Rhubella while the Perfecto Prep set fire to Duck Manor. Plucky escapes the inferno with Daff's help just as the manor is destroyed.
Batduck arrives at the "Narrowls" section of Gotham to aid the police, who are engaged in battle with psychotic criminals set free from ACME Looniversity by the Perfecto Prep (including Furball), meanwhile, The Scarecrow is defeated by Shirley. After saving Shirley, and intimating his identity to her, he leaves Buster in control of the Batmobile to stop the elevated train that is being used to transport the vaporizer to the city's central water hub. Batduck battles Rhubella, then escapes just as Buster topples the elevated line using the Batmobile's missiles, leaving Rhubella to crash with the train to the ground (" I won't kill you...but I don't have to save you").
Following the battle, Batduck becomes a public hero. Plucky gains control of Duck Enterprises and installs Calamity as CEO, firing Little Beeper. However, he is unable to hold onto Shirley, who cannot reconcile her love for Plucky Duck with his dual life as Batduck. Buster, newly promoted to lieutenant, unveils a Bat-Signal for Batduck and mentions a new criminal, a little girl that, like Batduck, has "a taste for the theatrical", leaving a Joker playing card at his crime scenes. Batduck promises to investigate and Gordon mentions that he forgot to thank Batduck for his efforts. Batduck replies by saying that he'll never have to, as he takes off into the night.
- Plucky Duck \ Batduck - Bruce Wanye \ Batman
- Shirley The Loon - Racheal Dawen
- Buster Bunny - James Gordon
- Rhubella the Rat - Ra's al Ghul
- Daffy Duck - Alfred
- Mary Melody - Scarecrow
- Calamity Coyote - Lucius Fox
- Furball - Victor Zsasz
- Montana Max - Carmine Falcone
- Roderick Rat - Ra's al Ghul
- Little Beeper - Wiliam Earle
- The scene of Plucky falling in the well references the comic "The Duck Who Falls".
- The scene of Plucky climbing the mountain references the comic "The Duck Who Falls".
- The scene where Plucky returns to ACME Acres in his plane references the comic "Batduck: Year One"
- The train builded by Plucky's father is a reference to "Batduck: Year One"
- The scene where Plucky does pushups while chatting with Daffy is a reference to "Batduck: Year One"
- The scene where the cops talk about the Batduck is a reference to "Batduck: Year One"
- The scene where Buster partner leaves him waiting in the car and takes money from a man in a market is a reference to "Batduck: Year One"
- Batduck's escape from ACME Looniversity (calling a swarm of bats) is a reference to "Batduck: Year One"
- The Batmobile was inspired by the comic "The Dark Knight Returns"
- The scene where Scarecrow appears on a horse is a reference to "Batduck: The Long Halloween"
- The final scene, where Buster and Batduck talk, is a reference to "Batduck: Year One"