Characters introduced this season:
New villains: Shredder, Krang (Teenage Mutant Ninja Turtles (1987)), and Preed (Titan A.E.)
Season 1 episode count: 16
Season 2 Episode 1: Enter the Shredder, Krang, and Preed
Synopsis: Team NegaOnett and their henchmen are back again, and this time, they have recruited their respective old partners in the form of Shredder, Krang, and Preed to plan revenge on Team Justice Ducks and their allies by kidnapping the female and children heroes, among them Michael D'Amico, Calves, Louie Walters Jr., and Regina Tightlips, resulting Fat Tony's gang to team up with the males of Team Justice Ducks and their allies to save the day.
Season 2 Episode 2: The Ding and I
Synopsis: When Team Justice Ducks and their allies are hired by Crash and Coco Bandicoot and their families and friends to help escort them to the Wumpa Islands to stop Dr. Neo Cortex, Uka-Uka, and his henchmen to see what they're up to, they soon discover that Dr. Nefarious Tropy has built a Time Bell that can travel through time, and to make matters worse, Team NegaOnett and their henchmen have planned on stopping Drake Mallard from becoming Darkwing Duck in the past, and it's up to Team Justice Ducks and their allies to stop them with help from the King of Time.
Season 2 Episode 3: 20,000 Leagues Under the Audubon Bay
Synopsis: When Team NegaOnett floods Duckburg and St. Canard with the Audubon Bay's seawater with Liverpool's help, Team Justice Ducks and their allies must find a way to restore the sea level to normal, while at the same time, help Megavolt and Louie Walters overcome their respective fear of water and sharks.
Season 2 Episode 4: Around the World in 80 Hours
Synopsis: Entering a Three Day World Grand Prix against Team NegaOnett, Team Justice Ducks race across Tokyo, New York City, and Rome to win a grand prize in the form of a power cell that gives the user extreme strength.
Synopsis: Based on the "Darkwing Duck" episode "My Valentine Ghoul," but with some twists. Sick and tired of being angry and jealous of Darkwing Duck, Sora, Hercules, Hubie, and Terra having Morgana Macawber, Kairi, Megara, Marina, and Aqua for themselves, Negaduck, Vanitas, Ratigan, Drake, and Pitch Black, while helping Team NegaOnett illegally mine some diamonds from Onett to create some super laser weapons that can freeze a target in its spot with an abandoned candy factory, end up deciding to seduce Morgana, Kairi, Megara, Marina, and Aqua into joining forces with them by tricking the five couples into an argument with fake taffy bubble messages disguising their voices as each lover's voice. And when the five villains, alone from the hidden plotting villains, successfully trick the five girls into believing that they've reformed, the five boys and their allies, knowing full well that it's a trick, decide to go along with it while trying to help the five couples reconcile via a date and handmade love potion. But while the five couples are, despite still arguing with each other thanks to the five villains' early trickery, struggle to find a way to reconcile with Team Justice Ducks and their allies' help, including the said love potion, they try to solve the mystery of Onett's missing diamonds.
Season 2 Episode 6: Journey to the Center of Pompeii
Synopsis: When the Mythical Treasure of Pompeii is stolen from a museum in Rome by Team NegaOnett and their henchmen, Team Justice Ducks and their allies follow them from the ruins of Pompeii to the Earth's core to discover a prehistoric world inhabited by dinosaurs.
Season 2 Episode 7: Toy Chaos
Synopsis: Based on the "Darkwing Duck" episode "Toys Czar Us." After Puppetmon is defeated twice for trying to steal other toy companies' toys to put his toys on shelves under Negaduck and Gygas' orders, he, along with them and Team NegaOnett, soon kidnaps the children of Duckburg and St. Canard, including the attempted interfering Michael's group, Megara, and Marina, to have them buy Puppetmon's toys in his forest toy utopia, and when Team Justice Ducks find out, they come to the rescue.
Season 2 Episode 8: The Mysterious Archipelago
Synopsis: When Xerneas' home island is in danger by Team NegaOnett and their henchmen by stealing the island's source of life, Team Justice Ducks and their allies must find a way to save the island and its archipelago from sinking beneath the sea.
Season 2 Episode 9: Komodo and Puppet Lumps
Synopsis: After Puppetmon and the Komodo Brothers get fired and banished by Team NegaOnett for accidentally nearly blowing up Negaduck's group's hideout with TNT and Nitro boxes while trying to show off a plan, the children of Team Justice Ducks and even the reluctant Team Justice Ducks and their allies take them in. But when they cause more harm than good when trying to help solve and stop crimes, Puppetmon and the Komodo Brothers are again kicked out. And when Team NegaOnett find out about this, will Team Justice Ducks and their allies find a way to escape their trap when Puppetmon and the Komodo Brothers are rehired by Team NegaOnett?
Season 2 Episode 10: Jungle Trek
Synopsis: After Team Justice Ducks and their allies, as well as Team NegaOnett and their henchmen, get separated in the Ursaring Jungle by a horde of angry Ursaring, they must temporally bury the hatchet against each other and work together in order to find each other and escape. But then Team Justice Ducks and their allies must rescue two Teddiursa siblings from Team NegaOnett and their henchmen's clutches after helping their Ursaring mother with the two cubs and the Ursaring horde's help.
Synopsis: While fighting Team NegaOnett and their henchmen as usual, Team Justice Ducks and their allies and the villains accidentally cause an accident that leads to Megara and Preed, Marina and Vanitas, Cream and Negaduck, Sonic the Hedgehog and Shadow the Hedgehog, and Megavolt and Quackerjack having their minds switched to the other's bodies.
Season 2 Episode 12: Cleanliness is Next to Slickiness
Synopsis: After Team NegaOnett's henchmen cause an oil spillage in Audubon Bay under Team NegaOnett‘s orders for some mysterious reason, Team Justice Ducks and their allies decide to not only clean up the oil spill, but also find out why Team NegaOnett would do that.
Season 2 Episode 13: Luck of the Duck
Synopsis: After Team NegaOnett imprison the Lucky Charms of Wumpa Island in Gygas' airship prison, they develop good luck for themselves, resulting Team Justice Ducks and their allies to have less luck. But then a miracle occurs when Fat Tony's gang, Michael's group, Hubie, Marina, Megara, and Hercules discover a way to stop it from secret help from the recently fired henchmen.
Season 2 Episode 14: One Duck's Clash is Another Day of Crimefighting
Synopsis: Based on the "Darkwing Duck" episode "Clash Reunion." When Dunce Spark, Blackthorn, Puppetmon, and Liverpool, under Team NegaOnett's orders, attack Drake Mallard's high school reunion to steal the Power Cells for Gygas' Power Guncannon, will Darkwing still save the day even after his mask is removed by accident that then shatters his confidence?
Season 2 Episode 15: Stress is the First Thing to Go
Synopsis: Based on the "Darkwing Duck" episode "Stressed to Kill." When everyone in Duckburg and St. Canard is seemingly hypnotized into being relaxed, Team Justice Ducks and their allies discover that Pitch Black, Dunce Spark, Blackthorn, Liverpool, and Puppetmon are causing this by using Puppetmon's Relaxi-Blaster to make people relaxed under Team NegaOnett's orders. And when Darkwing and Scrooge McDuck are zapped by it, they become too relaxed as well, and it's up to Team Justice Ducks and their allies to find a way to cure the relaxed-induced people, Darkwing, and Scrooge before Team NegaOnett cause more mayhem.
Season 2 Episode 16: Aurora's Borealis
Synopsis: When Team NegaOnett and their henchmen steal a portal mechanism to open a portal to Onett in an attempt to rule all dimensions by merging both dimensions together, which would cause the end of the world, Team Justice Ducks and their allies leap into action to stop them again, with help from Princess Aurora and Prince Phillip's special Borealis Portal Device bestowed to them by Ness' group.