The second film in the newly rebooted CGI Darkwing Duck franchise, this sequel picks up a few years after the first one.
Darkwing has made a name for himself in St. Canard. The inheritance he has received from the late Scrooge McDuck has allowed Drake Mallard to focus solely on crime-fighting, his egotistical and self-righteous personality unlikely to well serve him in the workplace anyway. He has a base of operations in the tower of the Audubon Bay Bridge from which he monitors the city, as well as a house in the suburbs that he shares with Launchpad McQuack, the two often bickering like an old married couple.
Darkwing's hands are full dealing with a never-ending rogues gallery, the most pressing villains currently being Quackerjack, a deranged prankster terrorizing the city, and Moliarty, a mole who has taken over the remnants of Taurus Bulba's criminal rackets which he oversees from his underground lair. Darkwing is usually successful in his pursuit of criminals and is loved by the public, and himself.
After being ambushed by government agents, as a test of his abilities, Darkwing is recruited into S.H.U.S.H., a secretive international espionage and law-enforcement agency overseen by Director J. Gander Hooter, an owl, and Vladimir Goudenov Gryzzlikof, a gruff and combative Russian bear and S.H.U.S.H.'s Deputy Director, whom Darkwing suspects of being a traitor, a suspicion Gryzzlikoff reciprocates. Hooter informs Darkwing that intelligence chatter indicates that F.O.W.L, a global terrorist organization masterminded by Phineas Sharp, a British vulture rarely seen or heard, is in the midst of planning something major.
Coincidentally, Drake Mallard's old friend Professor Waddlemeyer, who is still living in Duckburg, has been at work on the Tronsplitter, a device which can separate, duplicate, reduce or enhance negatrons and positrons. His home laboratory is raided by agents of F.OW.L., led by Steelbeak, a sinister rooster with a metal mouth. Waddlemeyer is killed trying to prevent his machine from being stolen, but with his dying breaths, he tells his now pre-teen granddaughter Gosalyn to seek out Drake Mallard / Darkwing Duck. Evading and out-witting agents of F.O.W.L. who are pursuing her, the spunky and precocious Gosalyn stows away on a train and travels east, showing up at the home of Drake Mallard and Launchpad.
Devastated by the death of his old friend, Drake agrees to lodge Gosalyn and protect her until other accommodations can be made. The two soon clash, as Gosalyn, a gifted archer, stows away on Darkwing's dangerous missions, craving to be part of the action and preoccupied with vengeance (much as young Drake was), while Darkwing is not pleased at the interruptions to his routine. Gosalyn finds a more supportive ally in Launchpad, himself a big kid at heart.
While Darkwing and Launchpad investigate F.O.W.L.'s fiendish plans with the Tronsplitter, an assignment that takes them to Europe, Asia, and the Caribbean, Darkwing finds himself becoming entangled with Dr. Sarah Bellum, an enigmatic scientist working for S.H.U.S.H., his old flame Morgana having abruptly and unexpectedly long ago left him to travel the world. But the closer he gets to Bellum, the less sure he is that she can be trusted.
Eventually F.O.W.L.'s plot is uncovered. They are using the Tronsplitter to create mass lawlessness by accentuating the malice inside everyone, and replacing world leaders with evil duplicates under their control.
Steelbeak is assisted in this operation by Dr. Reginald Bushroot, a once promising scientist and expert on DNA who many years ago accidently transformed himself into a half-plant, half-duck monstrosity by injecting himself with plant DNA while experimenting with photosynthesis. A decent duck slowly being driven mad by his condition, he is black-mailed into participating in F.O.W.L.'s global domination scheme with the promise of an antidote.
Throughout the course of the adventure, Drake and Gosalyn grow fond of one another, and Drake's selfishness begins to lessen as he decides to adopt her, seeing her as a kindred spirit.
Although victorious against F.O.W.L. in the end, during the climactic battle as the Tronsplitter is destroyed, Darkwing is severely wounded, and when he comes to, he realizes the full extent of the price he has paid. Weakened, and not fully himself, he learns he is about to go up against his most challenging adversary yet. One who knows all his tricks. His every strength, his every weakness, his every secret. Himself……….
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