Reginald Bushroot, a plant scientist, only wants to make the world a better place to live, but his colleagues mock his passion for plants. When he subjects himself to his own experiments, he becomes a half-plant, half-duck mutant, and now desires to get even with his tormentors.

• Title Reference: Beauty and the Beast
• Absent: Gosalyn

Bushroot tries to grow a wife for himself, but the result is not the flower that he expected.

• Title Reference: Night of the Living Dead

S.H.U.S.H. sends Darkwing, Launchpad, and Gosalyn to Africa to find missing famous anthropologist Dr. Beatrice Bruté. Darkwing discovers that Major Trenchrot is planning to open a vacation villa for villains.

• Title Reference: The Grapes of Wrath

Someone is stealing the money in Saint Canard by erasing all ink on the banknotes and leaving them nothing but worthless papers. S.H.U.S.H. Director J. Gander Hooter calls on Darkwing to help solve the mystery but chief Agent Gryzlikoff doesn't trust him. Darkwing discovers that the thief is Ammonia Pine, a woman who used to be a maid until some dangerous chemicals caused her to be obsessed with cleaning.

• Absent: Gosalyn

S.H.U.S.H. has given Darkwing Duck a case to travel to Oilrabia and stop Steelbeak. F.O.W.L.'s top agent is threatening to flood the country with a portable weather machine. The only problem is that Darkwing has agreed to let Launchpad assume the role as hero and be a sidekick himself for this mission.

• Title Reference: What a Way to Go!
• Absent: Gosalyn

Darkwing goes back in time with Gosalyn and he meets himself in grade school when he was known as "Drakey". He then sees a record shop being robbed by a gang of greasers. Due to Darkwing's inaction, Darkwing's present time gets changed when the duo comes back to the present. Therefore, Darkwing and Gosalyn must again go back to the past to restore it.

• Title Reference: Paradox (Dictionary definition: "a statement or proposition that seems self-contradictory or absurd but in reality expresses a possible truth.")
• Absent: Launchpad

Darkwing investigates a case in which money is disappearing along with the bank vaults. Bushroot creates a tree covered with money.

• Title Reference: Easy Come, Easy Go

Darkwing's computer goes haywire causing him to trade bodies with Gosalyn as do Launchpad and Honker. Now Gosalyn must pose as Darkwing to stop F.O.W.L.'s latest scheme – stopping the Earth's rotation in an attempt to blackmail the planet.

• Title Reference: Trading Places

Darkwing Duck investigates the production of a movie, which is plagued by accidents and turns out to be directed by none other than Tuskernini, who has abandoned his life of crime for the cinema.

• Title Reference: Hush… Hush, Sweet Charlotte

Jambalaya Jake and his alligator Gumbo, both from the bayou, have moved to the city after hearing it was "easy pickings". By using Launchpad as bait, they try and catch Darkwing. But Darkwing shows them first hand that in the city it is in fact no "easy pickings". Debut of Jambalaya Jake and Gumbo.

• Title Reference: Can't Buy Me Love
• Absent: Gosalyn

Drake takes Gosalyn on a camping trip to teach her about the great outdoors. However, the national park has been evacuated due to a monstrous bear controlled by Steelbeak that has been attacking both campers and wildlife alike.

• Title Reference: Bearskin Rug
• Absent: Launchpad

Darkwing goes undercover at a spa to root out a pair of workers responsible for a museum break-in. To his dismay, Herb and Binkie Muddlefoot tag along. The health spa owner, Jock, has discovered the formula for a fountain of youth. The last ingredient he needs is a feather from a true hero: Darkwing Duck.

• Title Reference: You Bet Your Life
• Absent: Gosalyn

Posing as a psychiatrist, Quackerjack convinces Darkwing that being a superhero isn't right for him. With Darkwing out of the picture, the criminal is free to go on a crime spree.

• Title Reference: Days of Thunder

To get revenge on Darkwing, Jambalaya Jake has Granny Whammy mix him up a hex. He mistakes Launchpad for Darkwing (while he is posing as Darkwing Decoy) and targets him with the curse. Now Jamabalya is using Launchpad as a partner in crime, and Darkwing is getting all the blame for it.

• Note: There are two versions of this episode: in the first, Jambalaya Jake lures Darkwing to a tower by having Gumbo bite a power line, in the second, Jamablaya Jake lures Darkwing to the power company by causing a blackout by pouring hot sauce into a telephone. Otherwise, the episodes are identical.
• Absent: Gosalyn

In this parody of Spider-Man, a mutated spider bite causes Darkwing to grow four extra arms. When this creates the hero trouble while trying to catch Moliarty, Darkwing adopts a new super-hero identity – Arachno-Duck.

• Title Reference: Arachnophobia

Gosalyn comes upon a spaceship that has crashed in the park. A cute alien emerges, wearing a rather restrictive collar which he doesn’t seem to be fond of. However, it turns out, that the extraterrestrial is actually a wanted criminal and Darkwing has to stop him.

• Title Reference: When Worlds Collide

Steelbeak teams up with agent Ammonia Pine to clean out banks for F.O.W.L. Gosalyn starts a Darkwing fan club.

• Title Reference: Cleanliness is Next to Godliness

As Steelbeak is stealing rubber duckies, Darkwing's attempt to stop him is interrupted by Comet Guy, a superhero from another planet who is looking for a hero to train him.

• Title Reference: Faster than a speeding bullet
• Absent: Gosalyn

Darkwing becomes fed up with the cold, so he decides to go on a vacation. But before he can, he finds out that banks are being robbed, with no forced entry.

• Title Reference: All's Fair in Love and War
• Absent: Gosalyn

Gosalyn and Darkwing are hyped over a video game competition involving the popular Whiffle Boy. However, a toy maker gone insane, Quackerjack, is out to get revenge on the video game industry that put him out of business. Both Darkwing and Quackerjack end up trapped in Whiffle Boy video game.

• Song: Whistle While You Work
• Absent: Launchpad

Morgana is using sleep sand to rob the citizens of St. Canard while they sleepwalk. When Darkwing steps in to set things right, he ends up in dreamland. Nodoff, controller of dreamland and supplier of Morgana's sleep sand wants the entire city to snooze, and will see to it that no one gets in his way.

• Note: Megavolt, Quackerjack, Bushroot, Liquidator, Steelbeak and Ammonia Pine makes non-speaking cameo appearance in Darkwing's dream.
• Absent: Gosalyn

When Quackerjack learns that parents won't buy his dangerous toys, he decides to create a toy utopia for children, with him as the ruler. Gosalyn gets into trouble at school, causing the principal to suggest Drake take a better look at his parenting. Drake gives up Darkwing to become the perfect parent just as Quackerjack executes his insane plot.

• Title Reference: Toys "R" Us

Gizmoduck comes to St. Canard to help stop Megavolt's latest scheme; stealing horseshoes and cable to build a giant electromagnet. Darkwing is hardly receptive and wallows in self-pity as Gizmoduck takes the spotlight.

• Title Reference: Up, Up and Away

While pursuing the Fearsome Five, Darkwing is thrown into a giant cake – which serves as a portal between his world and the Negaverse. In the Negaverse, everything is the extreme opposite of his world and Negaduck is supreme ruler, so Darkwing decides to use his new friends (The "Friendly Four") to change things a bit, which Negaduck does not like.

• Title Reference: Life, the Universe and Everything

Bud Flood, the crooked owner of a bottled water company, has been sabotaging his competitors' drinking water to promote his own. Darkwing moves to stop him, but Flood falls into a vat of contaminated water, only to survive and become a hydrokinetic mutant known as the Liquidator. Now, Liquidator proceeds to turn all of St. Canard's water hard and DW must stop him.

• Title Reference: Die Hard

Launchpad gains psychic powers, but has trouble controlling them. F.O.W.L. agent, Major Synapse, steals S.H.U.S.H.'s Nora Ray, and uses it on his underlings to give them super brain powers.

• Title Reference: Heavy Metal

Negaduck, disguised, frames Darkwing for a series of crimes. Thanks to S.H.U.S.H. director J. Gander Hooter knowing that Darkwing is innocent, he arranges for him to use an experimental S.H.U.S.H. design to go into hiding, which ends up causing him to spontaneously change into whomever he looks at.

• Title Reference: The Sky's the Limit

When Comet Guy returns, he tells Darkwing he needs him back on his planet. Darkwing thinks that he's going to have to save the planet, until he finds out that everyone on the planet is a hero, and they need him as their "ordinary guy," since the last one left. They want Darkwing to be their 'damsel in distress,' so that they'll have someone to rescue. But Darkwing gets fed up, so he tries to turn Comet Guy into a villain.

• Title Reference: Planet of the Apes
• Absent: Launchpad and Gosalyn

A crowd of pushy holiday shoppers rub Bushroot the wrong way. He decides to ruin Christmas by taking control of all of St. Canard's Christmas trees.

• Title Reference: It's a Wonderful Life

Megavolt's latest device accidentally transports him and Darkwing into the real world, where Darkwing Duck is only a cartoon.

• Title Reference: Switching Channels
• Absent: Launchpad and Gosalyn

Drake Mallard disappears and it’s up to the Crimson Quackette to find him.

• Title Reference: Dances with Wolves
• Absent: Launchpad

In a parody of the TV series Twin Peaks, Honker's parents go missing and all clues point to the mysterious town of Twin Beaks where mutant alien cabbages have begun their conquest of Earth.

• Title Reference: Twin Peaks
• Story Reference: Invasion of the Body Snatchers

Bushroot creates a new experimental fertilizer that causes plants to grow large and strong.

• Title Reference: The Incredible Hulk

Darkwing's refusal of Morgana's suggestion of help makes her very angry, which Negaduck sees as an opportunity.

• Absent: Launchpad

A nefarious criminal from the past returns, to profit by auctioning off a complete list of all of S.H.U.S.H.'s secret agents. J. Gander teams up Darkwing with the legendary Derek Blunt to intercept the documents before they fall into the wrong hands.

• Title Reference: In Like Flint
• Note: Steelbeak and Ammonia Pine, and Magica De Spell, the Beagle Boys, and Flintheart Glomgold from DuckTales make non-speaking cameo appearances.
• Absent: Gosalyn

To prevent the invention of the yo-yo, Quackerjack travels back to the medieval land of Canardia. Darkwing and Launchpad follow Quackerjack and find Herb and Binkie as King and Queen of Canardia. Posing as the king's advisor, Quackerjack convicts Darkwing as a warlock.

• Title Reference: "Rock of Ages"
• Absent: Gosalyn

During a battle between Darkwing, Megavolt and Quackerjack, Gosalyn ends up aboard the villains' Time Top, just before it starts up and takes them to the future. There, Gosalyn finds out that Darkwing has become Darkwarrior Duck, who enforces the law with an iron fist.

• Title Reference: Crime and Punishment
• Note: Some various villains makes cameo appearance.

Darkwing is constantly getting stressed, so he goes to a stress-free clinic (which is being run by Megavolt and Quackerjack), and they brainwash him. Now he is too calm (not even Gosalyn destroying the house can get him mad) when Megavolt and QuackerJack start a fire that soon starts to spread throughout the whole city, Launchpad and Gosalyn have to try to get DW out of his repressed state.

• Title Reference: Dressed to Kill

J. Gander asks DW to train some of S.H.U.S.H.'s agents. That does not go over well with Agent Gryzlikoff, who joins F.O.W.L. as a double agent. Steelbeak sets a trap for the newly titled "Darkwing Squad" while Gryzlikoff faces off against Darkwing.

• Absent: Gosalyn

When Binkie Muddlefoot gets hit on the head by a bowling ball, her inner "little hero" escapes and causes her to become the Canardian Guardian. Her endless quest for safety endangers Darkwing's life as he tries once again to capture Megavolt.

• Absent: Gosalyn

Bushroot creates a formula, intending to create an intelligent plant friend, and Gosalyn ends up sampling it. Now Darkwing has a limited amount of time to find a cure before Gosalyn melts into a pile of goo.

• Title Reference: I'm Okay, You're Okay

Darkwing's TV producer feels that Darkwing's TV show needs a new gimmick in the form of a spin-off character, which might really be Darkwing's replacement by Bushroot! This scheme is actually a scam by the TV producer to steal money from the show, since it is much cheaper to have a plant such as Bushroot as the main star than an actor such as Darkwing! Herb and Binke Muddlefoot are actors who have act of out characther ruthless business tycoons due to a hidden clause in their acting contract that "The Studio is always Right". The Muddlefoots and Bushroot get to ride in a limousine which Darkwing and Gosalyn have to sneak in the studio disguised as Donald Duck and Louie Duck! Only appearance of the Darkwing Duck fan club who recognize Gosalyn but not Darkwing!

• Title Reference: A Star Is Born
• Absent: Launchpad

Negaduck steals a diamond that can steal other people's powers. After he steals the powers from Bushroot, Megavolt, the Liquidator and Quackerjack, they have to use their weaknesses to stop Mega-Negaduck.

• Note: Gosalyn appears but does not speak.

It's Ammonia Pine's worst nightmare! FOWL has teamed her with her polar opposite, her filth-loving sister, Ample Grime. It would be easy for Darkwing Duck to stop them. But Gosalyn, not having enough allowance to buy a video game, has discovered that she can cash in whatever she recycles… including the Thunderquack's engine, the Ratcatcher, a few gas guns, etc.

• Title Reference: Thirtysomething

While investigating pizza topping crimes, Darkwing falls for a beautiful, creepy villainess called Morgana MacCawber.

• Absent: Gosalyn

Alien hats invade earth, take control of a slew of nuclear weapons, and demand to be made rulers of the universe. Debut of Flarg, Barada and Nikto.

• Story Reference: King Klaatu and two of the villains are named after the phrase "klaatu barada nikto" from The Day the Earth Stood Still

F.O.W.L. is at it again! This time, the fiendish organization is in control of the tides themselves. J. Gander Hooter teams up Darkwing and Gryzlikoff to foil the plot, and they end up fighting amongst themselves rather than getting to the bottom of things.

• Absent: Launchpad and Gosalyn

When Quackerware comes to life, S.H.U.S.H. thinks Herb Muddlefoot is behind it!! Drake investigates by joining in on Herb's Quackerware sales route.

• Absent: Gosalyn

In Darkwing's dream, the Fearsome Five, Steelbeak and Tuskernini are tired of defeats, and to get revenge on Darkwing, they futilely create a circuit machine to fix him.

• Absent: Gosalyn

F.O.W.L. rebuilds Taurus Bulba into a death machine, hoping to create a new agent from him. Bulba refuses their offer and burns only with the desire to have revenge on Darkwing, which includes kidnapping Gosalyn and Honker. To make matters worse, a recent accident has Darkwing in a wheelchair. Can he defeat a new and improved Terminator machine and rescue the kids in his condition?

• Title Reference: Terminator

Darkwing is to appear as the guest of honor at a comic book convention, while Splatter Phoenix terrorizes the town by "improving" boring art.

• Title Reference: "Ain't Misbehavin'"

Darkwing and Gosalyn go with Morgana to her old magic school, where she is to present her thesis paper. Gosalyn tries to find a shortcut to learning magic.Beelzebub tricks Gosalyn into casting a spell that sends Darkwing into hell where he is confronted with his worst nightmare-spending eternity with the Muddlefoots!

• Notes: This episode was banned from airing again after its initial broadcast because of its religiously sensitive subject matter, and is the only episode not re-released on home media in the US, being unavailable for purchase on the iTunes Store and Google TV, and unavailable to stream on Disney+, led to be locked away in the Disney vault. The Magic Brooms from Fantasia's "The Sorcerer's Apprentice" make a cameo.
• Absent: Launchpad

A news reporter wants to film Darkwing Duck on his cases. But she thinks what Darkwing is doing is too boring. So she becomes a villain for DW to fight to boost her ratings. Will DW be canceled permanently?

• Title Reference: Broadcast News

Gosalyn, working for her school newspaper, covers the three way battle between the Rubber Chicken, Cement-head and Darkwing Duck.

• Title Reference: Mutiny on the Bounty

Morgana opens up a new restaurant, but Darkwing forgets to cancel the guests coming there: The Cute Little Lost Bunnies! Meanwhile, Negaduck plans to turn the C.L.L.B. evil.

• Title Reference: "Alice's Restaurant"