Negaduck goes around town stealing and causing mayhem dressed as Darkwing Duck and frames him for all of it. The real Darkwing is rescuing a kitty out of a tree and sees a mob approaching. He realizes that they are an angry mob after him and runs. He sees a program on television and sees a report about how he has changed from do-gooder to evil villain. The mayor has offered a reward of a million dollars.
Darkwing barely escapes the mob and goes to S.H.U.S.H. headquarters. Agent Grizlikoff jumps on Darkwing planning on collecting the million dollar reward when J. Gander Hooter tells him that he knows that Darkwing is innocent. They go to the lab and see Dr. Sarah Bellum. She uses a machine that is supposed to alter Darkwing's appearance, but it does not cause him to change at first. Then suddenly he turns into a Grizlikoff look-a-like then a Dr. Bellum look-a-like. It only happens when Darkwing looks at someone and he changes into that person. Dr. Bellum tries to use the machine on Darkwing to change him back but it malfunctions.
Darkwing is determined to prove his innocence and heads to the police station on the motorcycle. Gosalyn and Launchpad are riding with him and he has to stop suddenly to keep from hitting a dog. They land in the bushes and Gosalyn and Launchpad see the dog with Darkwing's hat on and think that it is him and chase ofter it. Darkwing comes to and wonders why they are chasing the dog. Darkwing finds Negaduck and Negaduck grabs him. Darkwing sees a baby and changes into a baby. Negaduck thinks he can turn in the baby Darkwing and collect the reward when a crowd shows up. They think that Negaduck is Darkwing in disguise and jump on him. Baby Darkwing lands in the baby's stroller and changes back.
Darkwing finds his motorcycle and goes searching for Negaduck and finds him. They fight on the motorcycle and Darkwing changes into a cello player that he sees as they are speeding along. Negaduck wonders how he is doing that and they go flying off an unfinished bridge.
Meanwhile, Gosalyn and Launchpad have caught the dog and brought it back to Darkwing's secret hideout. Darkwing returns and asks them what is going on. Gosalyn and Launchpad now know that Darkwing is not the dog. Darkwing changes into Gosalyn and then Launchpad. Gosalyn asks for her dad back and Darkwing as Launchpad says he will find him and takes off in the Thunderquack jet. He changes back into Darkwing and crashes the jet onto Negaduck.
Darkwing gets back to the hideout in a shambles and thinks that he should give up. Gosalyn tells him not to give up and that maybe he should think like Negaduck to find him and capture him. Darkwing thinks it's a great idea and stares at a picture of Negaduck and turns into him. Unfortunately, this kinda backfires and Darkwing starts acting like Negaduck and destroys some things and then goes after Gosalyn and Launchpad. They are able to escape and then get Dr. Bellum and follow him to Negaduck's hideout. Both of them get into a sort of race of arms and Gosalyn, Launchpad, and Dr. Bellum come in. Dr. Bellum hits both of them with the ray and Darkwing turns back into himself and Negaduck turns into a canned fish mascot. Negaduck flops away and Darkwing chases him. Mayhem in sues as they both change into a lobster and a sailor. Darkwing changes into Gosalyn and hits a can with a paddle knocking out Negaduck.
The police show up after Darkwing is hit with the ray and turns back into himself for good. Darkwing shows them that Negaduck was behind all the crimes and they arrest Negaduck. Darkwing takes the ray gun and starts to walk off with it to dispose of it. He trips and it hits all the police men, Gosalyn, Launchpad, and Dr. Bellum and they all change into Darkwing.