The story opens on Dip Dopson reporting the start of St. Canard's annual Main Street Lit-Up Electrical Parade. He sees the parade's first float making its way down Quackenbush Tunnel and then notes that it is coming in rather quickly. As it turns out, Megavolt has hijacked the float, intending to "free" the "enslaved floats" of the parade. Fortunately, Darkwing and Launchpad are also on the float, with the latter trying to steer it despite that he doesn't actually have a driver's license. As Darkwing battles Megavolt, Launchpad notes to him that the nearby fountain is lit up, which gives the Duck Knight an idea. Shooting a grappling hook to a nearby street sign, he orders Launchpad to make a hard right turn, crashing the float into the fountain and shorting out Megavolt long enough for the cops to arrive. Later, as Megavolt is being loaded into a paddy wagon, one of the cops carting him in asks the other why the electric rodent is still wearing his chest plate. The distracted guard takes a look and is then knocked unconscious by his so-called coworker. The mallet-wielding "cop" then removes his helmet, revealing himself to Megavolt.
The next morning, Gosalyn informs Drake that he still needs to sign the permission slip for her class's field trip to the opening of St. Canard's new Maximum Security Penitentiary for the Criminally Crafty. Drake is peeved that he, as Darkwing, was not invited to the ceremony, since he caught every criminal imprisoned there. After Gosalyn leaves, Launchpad asks Drake if he wants to go to the aeronautics museum, but Drake orders his sidekick to fire up the Thunderquack.
At the new penitentiary, Warden Dullerd is showing Gosalyn's class around. Honker thinks that it might not be a good idea for them to be touring the place, while Mortimer L. Marquand (who is still doing community service for his misdeeds as Cat-Tankerous) expresses that he's just glad to be out of the house for a while. The warden brings the kids into the "General Population" area, where the students (and the readers) are shown that each villain is kept in a specially modified cell that nullifies their respective powers. Dullerd then suddenly has to cut the tour short because "their final guest" has arrived and he has to give the press conference about the prison's opening. As Megavolt is brought in, Warden Dullerd says that with the last super-powered villain locked up here, St. Canard should be safe for the future. But just then, the guard bringing Megavolt in removes his uniform, revealing himself to be Negaduck, having inexplicably returned to his original form after being turned into molecules in his last (canon) appearance.
As Negaduck takes out all the guards and scares off most of the people attending the press conference, Gosalyn tells her classmates to run for the exits, but then notices that Mortimer has gone missing. Darkwing soon shows up just as Negaduck jabs a giant pin into Megavolt's chest plate, causing a big electrical surge. Negaduck then exposits that the facility goes into lockdown if it registers an attack like the electrical one he just set off. The prison promptly does that, locking Darkwing and Gosalyn inside, and to make matters worse, Negaduck presses a button that unlocks the cells of all the criminals. As Darkwing is surrounded by all the villains, Negaduck gloats that they're going to give him thirty minutes to escape, after which they will come after him.
While Launchpad is busy trying to break into the prison to help Darkwing, Negaduck decides it is now time to send all the crooks out to defeat Darkwing, despite Tuskerninni pointing out to him that it has only been twenty of the thirty minutes he gave Darkwing earlier. ("Eh, what can I say? I'm a villain.") Darkwing, meanwhile, makes his way into the washroom and is suddenly attacked by Liquidator. In the ensuing battle, Liquidator accidentally knocks a shelf of soap bottles onto himself, allowing Darkwing to escape down the garbage chute. In the garbage, Darkwing finds himself up against the massive mass of mud known as Muckduck (making his first fully-seen appearance here). Darkwing escapes with Muckduck in pursuit and comes upon Ammonia Pine, who happened to be waxing the floors. Darkwing slides right away from Ammonia, leaving her to get consumed by Muckduck's attack.
Gosalyn, in the meantime, is crawling around the air vents, listening in on a conversation between Tuskerninni and Chronoduck, who are watching Darkwing's battles on the monitors. Trying to find a way to help her dad and also locate Mortimer, Gosalyn makes her way into the prison's kitchen and encounters Lilliput. The shrimpy villain attempts to capture her, saying that Negaduck is offering a spot in his new crew to anyone who takes Darkwing out, and he might pay just as handsomely for "Darkwing's number one fan". However, Gosalyn easily manages to defeat Lilliput and tie him up in tin foil.
Meanwhile, Darkwing has just tied up three of the Beagle Boys when a suspiciously yellow-eyed Launchpad suddenly appears, claiming that he barely made it into the penitentiary right when Negaduck put it into lockdown. Darkwing gets to work on bypassing a nearby electronic lock and hands "Launchpad" a crime-fighting manual he's been working on. "Launchpad" then prepares to strike him with a monkey wrench, but Darkwing quickly turns around and blasts gas into "his" mouth, saying he knew this wasn't the real Launchpad because "Launchpad doesn't do exposition." Camille Chameleon, now revealed, starts battling the Duck Knight, seemingly getting the upper hand when she shape-shifts into an octopus form resembling Ursula. She brags that her powers have grown since their last encounter, but as Darkwing figured, she is still weak to being exposed to intense heat, which he pulled off by sticking Quackburn's Fast-Heating Ouchie Strips on her back. With Camille melted down to a blob, Darkwing walks off, unaware that he left the heating strips right in front of the frozen Isis Vanderchill. Unfortunately, right after he takes Ample Grime out of commission, Darkwing is captured by some hypnotized guards and brought forth to Constance A. Dention, who's now going by the name Mistressterious.
Elsewhere in the prison, Mortimer wanders into solitary confinement and comes by the cell inhabited by Fluffy, who is hiding in the shadows. Fluffy recognizes Mortimer as Cat-Tankerous, but Mortimer says he's just a wimpy little kid who doesn't even know how to deal with bullies, let alone actual supervillains. Fluffy, interested in Mortimer's mention of the unstoppable armor suit he used to have, offers a deal with Mortimer. Mortimer then lets himself be captured by Pokerface and demands to be brought to Negaduck. Negaduck is overseeing as Cement Head punches away at the floor to reach the power lines under the prison when Pokerface brings Mortimer to him. Mortimer says to Negaduck that he wants to be a bad guy like them. Negaduck doesn't take him seriously and orders Megavolt to get rid of him, but after Mortimer actually gives Megavolt a good thrashing, Negaduck decides maybe he could make Mortimer his understudy. Just then, Chronoduck calls Negaduck to look at something he and Tuskerninni just caught on the monitors. They show him footage showing that Rabbit-Racer was just about to catch Darkwing, but failed because is shoelaces were tied together by Gosalyn. Negaduck, recognizing Gosalyn on the monitor, orders the other villains to forget about Darkwing for now and go capture her.
Darkwing is now trapped in the illusions being cast by Constance A. Dention, now calling herself Mistressterious (which Darkwing remarks is an even worse name than her previous alias, "Suff-Rage"). Constance, transporting them into a pirate ship illusion, prepares to make Darkwing walk the plank when he refuses to surrender to her. However, her illusions are suddenly cut short when she is frozen by the now-defrosted Isis Vanderchill. After changing into a new outfit and hairdo, Isis goes after Darkwing to kiss him and ends up getting her lips stuck to a metal pole that he'd placed his hat and cape on while she wasn't looking. Darkwing then leaves to find Gosalyn...
...who is currently battling the combined forces of Bushroot and Dr. Fossil. It is shown that the two mad scientists have been creating small plant/dinosaur hybrids within the confines of the prison, but Gosalyn is now sending said creatures out against them. Bushroot then makes the mistake of saying that the plant-dinosaurs are small because he and Fossil only gave them a single drop of water. Upon hearing this, Gosalyn grabs a nearby fire hose and splashes the plant-dinosaurs, growing them to a larger size. With the duo subdued by the dinos, Gosalyn then takes the fire hose with her to the prison cafeteria, where she finds Darkwing battling One-Shot. Just as One-Shot gets the upper hand by pinning Darkwing to the wall with a spoon, Gosalyn promptly hits him with the hose too. One-Shot prepares to strike back, but is unable to because he has nothing but spoons (something he already threw at Darkwing) to use as his weapons, allowing Darkwing to punch him out.
Just as Darkwing and his daughter have reunited, Liquidator suddenly springs from the hose Gosalyn has been carrying and captures them. Liquidator brings the two to Negaduck, who introduces his new weapon - a giant electromagnetic projectile launcher he calls the Railgun, which is hooked into the grid underneath the prison (which used to be the St. Canard Power Plant before Launchpad converted the city to solar power at the end of Darkwing Duck: The Definitively Dangerous Edition). Negaduck explains that he's going to fire a projectile strong enough to break down the prison's walls, thus unleashing all the criminals on St. Canard at once. He also offers to make Gosalyn his heir, since he thinks she has evil tendencies (unlike his universe's Gosalyn), but she refuses.
Negaduck orders Mortimer to tie Darkwing and Gosalyn up to a hook that positions them in front of a giant target that the Railgun is aiming at. Mortimer does so, but not before slashing at Darkwing's necktie. Fortunately, though, it's then revealed that he was actually secretly helping them by doing this, as he also cut through the ropes that they were tied up in, allowing them to break loose. Just as Negaduck orders Megavolt (who's boosting the pulse on the Railgun) to fire the trigger, Darkwing then shoots a boxing glove from his gas gun, knocking him out and causing the Railgun to instead blast a hole in the roof. Negaduck has Liquidator destroy the water pipes, causing the prison to flood, which would allow the villains to reach the roof. As Darkwing escapes with Gosalyn and Mortimer in tow, he is suddenly caught by Isis Vanderchill again. Darkwing promptly tosses Isis into the water, freezing it and trapping the villains before they can escape.
Later, Warden Dullerd informs the press that the villains are all now back in their cells, crediting the work to his staff and saying that Darkwing provided "minor help", and insisting that the prison is still escape-proof. As he says this, he is completely unaware that Fluffy is no longer in his cell, and that Negaduck is right behind him, getting a cup of coffee. From his cell, Megavolt asks Negaduck why he's still here. Negaduck answers that he's "playing the long game" now and is going to use the prison as a new secret base of operations. Meanwhile, at the Mallard household, Drake and Launchpad are watching Derp Derfson finishing up his TV report about the crisis at the prison. Drake says to Gosalyn that he figures Mortimer will probably steer clear from the path of villainy from now on... unknowning that Mortimer has helped Fluffy sneak out of the prison.
- In addition to the villains mentioned in the above synopsis, other villains at the penitentiary include Clawed Hopper (from the Disney Adventures comic "Cereal Crimes"), Professor Moliarty, Hotshot (oddly without Flygirl this time), The Bug Master, Hammerhead Hannigan, Jambalaya Jake, Phineas Sharp, Wolfduck (from the Darkwing Duck NES game), and Anna Matronic.
- Quackerjack and Splatter Phoenix are among the villains seen in the crowd on the cover to issue #3 (pictured at the top of this page), despite that neither of them actually appear in this story.