I always thought the fourth and final season of Darkwing Duck should be as followed since Darkwing was canceled (I think).
Ep 1-3: Negaduck still trapped in limbo after going to the Negauniverse finally breaks free and finds himself in the 1930s....in the city of Cape Suzette where the series Talespin takes place. Upset he's in the past, he decided to stake claim of the city by taking over Shere Kahn's empire by robbing him of his money.
Meanwhile back in present day St. Canard, Darkwing, Launchpad, and Gosalyn are in the Thundequack flying around the city checking to see if there's any crime. Also there's a thunderstorm. The Thunderquack gets struck by lightening (think Back to the Future 2), and is sent back in time to the 1930's in Cape Suzette. Darkwing and company are thrown in jail by Baloo and Rebacca after both noticing he's the criminal that is robbing Shere Kahn from his money. Darkwing and company are confused but after a series a crimes, the police come to the conclusion that Darkwing is not the one they are after. Darkwing finally realizes it's Negaduck, and he, Launchpad, Gosalyn, and the Talespin series characters have to stop him.
In the end they do and finally are able to get back to the present in St. Canard, however, their victory is short lived when Negaduck escapes.
Ep4-6: Darkwing and company are back but realize they've been gone for a week. The city has been overrunned by criminals. The city finally realizes they need Darkwing Duck because without him the city will go under. Darkwing gets the praise and recognition he's been wanting for for years.
Meanwhile, the Fearsome Four have been rampaging the city. Still bummed about not knowing where Negaduck has been all this time, they decide to steal more stuff until Negaduck finally comes back. Negaduck catches up on the events but is upset to find F.O.W.L has also laid claim to the city. Negaduck says there are two things stopping him from taking over the city: Darkwing Duck and F.O.W.L. Negaduck and company plan on stopping F.O.W.L which leads to a confrontation with Steelbeak and the F.O.W.L Eggmen. Darkwing, Launchpad, and Grizzlikof stop them all.
F.O.W.L has taken a major blow thanks to Negaduck. However, Negaduck has escaped again but the rest of the Fearsome Five are taken away to jail for good along with Steelbeak.
Ep7: A filler episode where Darkwing and Morgana finally get married although Mayhem ensures with Morgana's family. At the end, Darkwing asks why Morgana is upset after they got married. Two things she says 1.) she wants Drake to retire now because she doesn't want him to be put in danger, and 2.) there's been recent problems with a sister of hers that has been disowned by her family, but doesn't want Drake to know anything else about it.
Ep 8-9: Drake announces he's going to take his wife's advice and retire. Meanwhile, the Muddlefoots are moving away after Herb find out he's been promoted and is going to be on the other side of the country. Drake is delighted but Gosalyn and Honker are saddened as they're going to miss each other.
However, after a series of problems at the company he works for, Herb finds out he is now been fired, so he is not moving away but now has to find another job. Honker and Gosalyn overhear from Herb talking to his wife that he thinks it's someone from his office that was jealous of his promotion. Gosalyn and Honker decide to do some investigating as their alter egos one last time despite that Morgana finds them and forbids them to go. However, the do anyway and get captured.
Herb, Binkie, and Drake are in a panic when they can't find their kids. Morgana tells them Honker and Gosalyn went investigating at Herb's old office after overhearing him about his problem with a person at work.
Drake tells Herb and Binkie that he'll get the kids back and dawns Darkwing Duck one last time. He and Launchpad rescue the kids, and Herb's co-worker is thrown in jail. Herb is cleared and is now going to move. Morgana (now acting as Gosayln's step mother) punishes her and tells her never again to do anything foolish. Drake agrees as he now finally realizes this isn't the life his family should have to endure and finally retires as Darkwing Duck.
Honker and Gosalyn say their goodbyes and Drake tells his family he's going to miss the Muddlefoots as he sees them drive off to their new lives.
Ep 10: It's been a few weeks since Drake retired from fighting crime. He's trying the best he can to cope with the situation even though there is still crime going on. He informed S.H.U.S.H and the agency informed the city of St. Canard that Darkwing has retired.
There's been someone from St. Canard police that has been hoping that Darkwing would retire so he could pickup where Darkwing left off. Although the police officer has been praised for his ability to catch criminals quickly, he's also harsh and somewhat brutal.
After criminal after criminal gets locked up and also fearing for their lives by this police officer, J. Gander Hooter makes a plea with Drake to investigate as Darkwing Duck after one of the higher ups in the police department contacted him. Drake says no and tells him to send Grizzlikof to investigate. After Grizzlikof does investigates, he also in thrown into jail. Hooter informs Drake about the Grizzlikof lockup, and after Morgana and he discuss the situation, Drake goes back as Darkwing one last time. He has a confrontation with the police officer who is now going by a crime fighting name and wants Darkwing to join with him. Darkwing states he fights crime, not scare criminals after they've been locked up fearing for their lives. The new crime fighter decides to fight Darkwing as he would be a thorn on his side. However, Darkwing wins in the end and the questionable new crime fighter is thrown in jail. (This story is inspired by the Batman animated episode Lockup)
Ep 11-12: Drake is enjoying his retirement yet again, or so he thinks. He, like the rest of the city, have been wondering why St. Canard have been getting a lot of earthquakes since St. Canard doesn't get any. There have been some small ones and some big ones. Drake thinks Professor Moliarty is behind it since he hates the surface world, but he hasn't seen the villain in years.
However, it's Taurus Bulba. His plan is to bring the city to it's knees with a new invention he stole from F.O.W.L. after the organization got taken down by Negaduck that causes major earthquakes. He wants to control the entire city. He also wants to destroy Darkwing Duck but has heard he has retired. Upset about the information, he decides to target Darkwing's daughter, Gosalyn. He sends his henchmen around the city to find her. After they do, Taurus goes on television informing the citizens it is he who has been causing the earthquakes. He then causes a massive earthquake that destroys several buildings downtown and informs the city council they have one day to surrender to him. Bulba also shows Gosalyn being locked up and tells Darkwing to come and get her or he will tell the city the identity of Darkwing Duck which would make Drake a target for everyone.
Morgana finally realizes no matter how many times Drake retires, the city will still need Darkwing Duck. Darkwing and Launchpad find out Bulba's location, and Darkwing has his last confrontation with Bulba before the robotic Bull is finally done away with. He rescues Gosalyn and the mayor gives Darkwing a key to the city with the citizens applauding.
However, Morgana is contacted by her father and is told that her disowned sister has resurfaced in Duckburg where she has caused problems in the past. He informs her that she needs to go and try to stop her.
Ep 13-16: It's been a rough ride the last month and Drake wants a vacation. Morgana having been informed from her father about her sister, tells Drake they should go to Duckburg. Drake agrees and Launchpad decides to contact Scrooge McDuck to see if they can stop by for a visit sometime while they're there.
Meanwhile on the outskirts of DuckBurg, Magica De Spell has tapped into a new form of black magic that will make her nearly invincible but needs Scrooge's lucky dime in order for the spell to work but doesn't know how to break in.
Drake, Morgana, Gosayln, and Launchpad arrive in Duckburg and go to McDuck Manner. Exchanges take place as Scrooge is happy to have Launchpad in his company for a short time before he goes back to St. Canard.
Morgana tells Drake she wants to see some of the city by herself as an excuse but secretly goes to find where her estranged sister is. She gets kidnapped by Negaduck who is in town and wants to rob Scrooge's money bin. Negaduck makes his way to Magica's hideout since the two are old friends. He says he can disguise himself as Morgana's husband to steal the coin for her as he also wants to have some of that magic so he can use it to steal the money from Scrooge. Magica agrees even though both will double cross each other. (end of part 1)
Drake, Launchpad, Gosalyn, and the DuckTales gang are visiting different places in Duckburg. Drake wonders where Morgana is since she hasn't checked in for several hours but figures she's probably shopping. They find the Beagle Boys up to no good as they're on a crime spree and are robbing shops. Drake changes into Darkwing and takes down the Beagle Boys (Bigtime, Baby Face, etc.). However, Darkwing has been set up as the Beagle Boys were just a ploy set up by Negaduck to draw in Darkwing. Darkwing is taken down by Negaduck in an abandoned budiling, captured, and changes into Drake Mallard thanks to Magica. Darkwing and Morgana exchange words after she informs him of her sister and what she and Negaduck are planning to do. Negaduck acting as Drake Mallard is now back with the others and heads home (end of part 2).
Negaduck acting as Drake steals Scrooge's dime easily and Magic appears. She casts her spell using the dime and now becomes the most dangerous and powerful person in the world. She also takes down Negaduck but he has informed her through some light studying he did back at her place that he can channel Magica's new power and make it his own. He does and leaves Magica powerless. He destroys McDuck Mannor and goes after Scrooge's moneybin.
Darkwing and Morgana break out of the abandoned building and team up with Gizmoduck as all three stop Negaduck (Morgana using a spell to take away Negaduck's power). Negaduck is captured by the police and is sent to a high security prison where he can't ever break out. Magica is taken back by Morgana's family to the underworld as they inform everyone that Magica won't be a problem anymore. Scrooge has deduced that Darkwing is Drake as he is no where around at the moment and secretly tells Darkwing, but tells him it will be his secret.
The Mallards then enjoy the rest of their vacation in Duckburg before J. Gander Hooter tells Drake to get back to St. Canard as he is needed there to stop a crime.
Darkwing and company leave in the Thunderquack and depart back to St. Canard.
*Series ends there*
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