Characters introduced this season:
New allies: Spike, Ember, Discord, Gilda, Karl, Lokina (My Little Pony: Friendship is Magic), the Mane Eight, Stallion Eight, Dazzlings (My Little Pony: Equestria Girls), and Gangreen Gang (The Powerpuff Girls (1998))
New villains: Dr. Eggman, Orbot, Cubot, and Tribot (Sonic the Hedgehog franchise)
Season 3 episode count: 18
Season 3 Episode 1: Hard-Boiled Eggman
Synopsis: When a mad scientist named Dr. Eggman and his robot goons, Orbot, Cubot, and Tribot, are hired by Team NegaOnett to help in stealing equipment to reactivate Gygas' battleship in Onett due to it losing power in its flight and weapon generators from the power cells being destroyed at the end of last season's final episode upon being sucked into Onett, they steal a Mediscepter back on Earth to reactivate the battleship's power cells, but when Hercules and Fat Tony are blasted by its deadly laser, falling into a coma, it's up to Team Justice Ducks and their allies, including Michael D'Amico, Legs, Louie Walters, Johnny and Regina Tightlips, Calves, and Louie Walters Jr., to get the Mediscepter to save them both.
Season 3 Episode 2: Green with Happiness
Synopsis: When Team Justice Ducks and their allies meet some fans in the form of Spike, Ember, Discord, Gilda, Karl, Lokina, the Gangreen Gang, Dazzlings, Mane Eight, and Stallion Eight, they agree to accompany them on a cruise to Hawaii. But when Team NegaOnett send their henchmen to steal a rare Tiki Idol to repower Gygas' battleship's power cells, it's up to the heroes, upon arrival in Hawaii, to stop them.
Season 3 Episode 3: All's Bell that Ends Bell
Synopsis: When Team NegaOnett's henchmen, under Preed's idea, use Dr. Nefarious Tropy's Time Bell to travel to the past to steal a power cell that can reactivate Gygas' battleship's power cells in the outskirts of 1950s Roswell, New Mexico, it's up to the children of Team Justice Ducks, Michael's group, Tempest Shadow/Fizzlepop Berrytwist, Party Favor, Kiki, Jiji, and Tombo to stop them alone.
Season 3 Episode 4: Bug Off Part 1
Synopsis: While helping Megara renovate her apartment, Team Justice Ducks and their allies discover with Megara and Hercules a strange artifact her uncle Troy left her, before he disappeared a year ago to find an alternate dimension to bring her home a souvenir, that ends up teleporting them to an alternate dimension called Insectacon where hostile giant insects rule, and after meeting and reuniting with Troy, who is still alive, but trapped, all this time, they must find a way to get back to their dimension when they learn from Troy's recent discovery that a jungle temple has the same artifact called the Dimension Top that can take them back home. (Team NegaOnett and their henchmen make a brief cameo appearance at the very end of this episode)
Season 3 Episode 5: Bug Off Part 2
Synopsis: After learning that Team NegaOnett and their henchmen have captured the Insect God and Goddess to use their magic to repower Gygas' battleship's power cells, Team Justice Ducks and their allies, Troy, Megara, and Hercules end up also discovering that the reason the insects were acting hostile to outsiders from beyond Insectacon is because they believe outsiders will destroy their home and Insect God and Goddess due to the Insect Vizier claiming Troy as the attempted murderer of the Insect God and Goddess three years ago, or a year ago in Earth and Onett's case. Now it's up to the heroes to convince the insects to trust them if they're to save the Insect God and Goddess and Insectacon and getting the heroes back home to their dimension.
Season 3 Episode 6: Bug Off Part 3
Synopsis: After arriving at Team NegaOnett's fort with the insects' help, Team Justice Ducks and their allies, Troy, Megara, and Hercules, right after Hubie, Marina, and the news crew, except J. Jonah Jamieson, finally arrive in Insecticon by decoding the artifact with Homer and Marge Simpson's help, work together with the insects to shut down the security system and break the Insect God and Goddess out. And after that's accomplished, the Insect Vizier reveals his true colors by revealing that he betrayed Insectacon three years/a year ago with Gygas' group's help. Now, it's up to the heroes and insects to stop Team NegaOnett and Insect Vizier from destroying Insectacon and other dimensions with the Dimension Top. But when the Insect Vizier double-crosses Team NegaOnett and their henchmen for power, both heroes and villains decide to temporally bury the hatchet to help the insects stop him.
Season 3 Episode 7: Bug Off Part 4
Synopsis: After the Insect Vizier's defeat and the villains getting away secretly back to Earth and then Onett, Team Justice Ducks, their allies, Troy, Megara, Hercules, and the news crew celebrate with the insects and after that's done, the heroes finally return home to Earth, promising to treat harmless insects such as butterflies with respect, and upon their return, they learn that they've been gone from Earth for three hours while they were in Insecticon for three days.
Season 3 Episode 8: Fourth of Fly
Synopsis: While preparing for a Fourth of July barbecue regardless of a heatwave hitting Duckburg and St. Canard, Team Justice Ducks and their allies discover Team NegaOnett has stolen an Anti-Gravity Cannon and plotting to use it to levitate the world for eternity. And with the Anti-Gravity Boots' help, it's up to the heroes to stop them.
Season 3 Episode 9: Charmy Takes the Cake
Synopsis: When Charmy Bee wakes up in the morning to discover everyone is ignoring him and not knowing his birthday for some reason, he thinks everyone doesn't care for him or remember his birthday, making him run away. But when Sonic the Hedgehog's group convince Charmy that everyone does care for him, he returns home and discover that everyone is actually ignoring him and pretending to not know about his birthday because of his surprise birthday party. And soon, he is not only in for a treat, but also in an ultimate battle against Eggman's bomb-throwing robots, courtesy of Team NegaOnett.
Season 3 Episode 10: Darkwing Doubloon of the Seven Seas
Synopsis: Based on the "Darkwing Duck" episode "Darkwing Doubloon," but with twists. Years ago in the time of pirates, after Captain Negaduck and Admiral Gygas' groups and their crew, in the form of the NegaOnett Pirate Crew, steal King Phillip and Queen Aurora's treasure, kidnap Okino and Kokiri Witherspoon, and sink their ship, Darkwing Doubloon and his Justice Ducks Crew and their allies decide to fight the villainous pirates to rescue Okino and Kokiri, get the treasure back, and get Phillip and Aurora a new ship. (No villains appear in the present day in this episode, just in the story of Darkwing Doubloon as told by Drake Mallard)
Season 3 Episode 11: Cats, Cats, Everywhere
Synopsis: When Team NegaOnett and their henchmen use a line of garbage trucks to kidnap cats of every shape and size, across Duckburg and St. Canard in order to lure Team Justice Ducks and their allies into a trap, it's up to the heroes to stop it.
Season 3 Episode 12: Adventures in Dragonsitting
Synopsis: While helping Megara and Hercules babysit Spike and Ember, Team Justice Ducks and their allies soon discover Team NegaOnett plotting to rob a botanic laboratory of a Prism Rose that'll power up Gygas' battleship's power cells, and they resolve to stop them and help Spike and Ember when they run off to prove they are more than just cowardly sidekicks.
Season 3 Episode 13: Dogs, Dogs, Everywhere
Synopsis: Discovering Team NegaOnett and their henchmen are redoing the same plot they did with kidnapping cats by kidnapping dogs instead with a line of garbage trucks, despite Preed's objections at first due to his allergies to dogs, Team Justice Ducks and their allies then have Toto help them outwit the new and improved plan by pretending to get caught and captured.
Season 3 Episode 14: Super Bebop, Koala, Pinstripe, and Puppetmon and Mighty Rocksteady, Dunce Spark, and Komodo Brothers
Synopsis: When Team NegaOnett create smarter and powerful robot replicas of Bebop, Koala Kong, Pinstripe Potoroo, Puppetmon, Rocksteady, Dunce Spark, and the Komodo Brothers to help in resetting up the Mesmerizer to control the minds of Duckburg and St. Canard, it's up to Team Justice Ducks and their allies to stop them again.
Season 3 Episode 15: Cookin' Up a Winterstorm
Synopsis: When Team NegaOnett unleash an eternal winter onto Duckburg and St. Canard by using a powerful Freeze Ray that can easily freeze the sun, Team Justice Ducks and their allies resolve to take action and stop it, despite dealing with Tiny Tiger, Dingodile, the Gangreen Gang, and Fearsome Four's colds.
Season 3 Episode 16: Mutagen Bull
Synopsis: After a train accident causes spilled chemicals to mix and create Mutagen, two cows drink some and, by the Mutagen's effects, merge to become an unstable angry and dangerous mutant bull, and it's up to Team Justice Ducks and their allies to return the mutant to its two normal cow forms again before Team NegaOnett can capture it and place it under their control.
Season 3 Episode 17: The Big Power Up
Synopsis: After Team NegaOnett finally repower Gygas' battleship's power cells by stealing the Impervium, it's up to Team Justice Ducks and their allies to find a way to stop their plans for dimensional domination.
Season 3 Episode 18: The Big Power Down
Synopsis: Discovering a way to defeat Gygas' battleship and the Impervium, as well as get Team NegaOnett and their henchmen into jail, Team Justice Ducks and their allies face off against the enemy in a dimensional portal lane to determine the fate of all dimensions.