Darkwing Duck and Launchpad McQuack are wrapping up a night of crime fighting when Launchpad wants to get something to eat. They go to a Hamburger Hippo stand and Launchpad takes off his scarf to eat so he won't get any stains on it. Launchpad finishes and they begin to head home. Launchpad then remembers that he left his scarf at the Hamburger Hippo stand and they go back to get it. They get to the spot where the place should be and find that it has disappeared. The cook tells them that he heard a noise out back and went to see about it. When he turned around to go back, the building was gone. Darkwing starts searching for clues as other buildings disappear around him without him noticing. As they are about to wrap things up, Launchpad notices that his other hamburger is gone and sees it being carried off by ants. He tries to get his burger from them, but is unsuccessful. Our heroes head home and we find out that the ants are under the control of a villain whose name is Lilliput. He is shrinking the buildings down to miniature size and putting them in his mini golf course.
Darkwing and Launchpad are sleeping in when Gosalyn and Honker bust in and Gosalyn insists that Darkwing take her and Honker to Goony Golf like he had promised. They go, although Darkwing (who is not in costume and is going as Drake Mallard) is basically falling asleep before the first hole of golf. After a few short scenes of mini golf, Drake falls asleep behind one of the buildings. He rolls down a hill and slams into the Hungry Hippo stand that has been miniaturized. He changes into his Darkwing Duck disguise and is immediately shrunken by Lilliput's ray gun. He at first thinks that he is dreaming until he pinches himself and realizes that it is real. He is knocked into the Hamburger Hippo stand again by a snail. Some of the ants are there and Darkwing takes off. Once he gets away from the ants, he is almost stepped on by Gosalyn. He tries to get Launchpad's attention by climbing on a gold ball, but Launchpad doesn't see him and hits the golf ball. Darkwing is able to dodge one building, but is clobbered by one of the fan blades on the miniature windmill.
Lilliput is directing his ants with one of the buildings and once they set it down, he learns that Darkwing has gotten away. Lilliput gives the ants some miniature dune buggies to chase down Darkwing.
Darkwing attempts to use his cape and glide over to Launchpad and get his attention, but Launchpad thinks that he is a bug and swats Darkwing away. Darkwing lands on the ground and hears a noise. The ants in the sand buggies have found him. After a short scene, Darkwing is able to once again get away from the ants. After dodging the ants, Darkwing accidentally rides up a dinosaur statue and is thrown into a bank building. After he has landed on the bottom floor, he sees more ants coming and hides. The ants come in and rip the safe off of the wall. They carry the money out onto a truck and Darkwing hops on as they drive away. The ants take the money to Lilliput who unshrinks it. Lilliput sees Darkwing and tries to smash him. He misses and accidentally flings Darkwing when he steps on a gold club. Darkwing lands on Honkers glasses and is finally recognized. Launchpad, Gosalyn, and Honker bring a miniature Darkwing to the main building where Lilliput is in an attempt to stop him. Gosalyn is able to knock the shrink ray out of Lilliput's hands and he then uses his ants to attack our heroes. Lilliput gets his hands on the shrink ray and shrinks Darkwing down to the of a germ. Gosalyn and Honker use a couple of shaken up soft drinks to get rid of the ants. Just as Lilliput is about to use the shrink ray on our remaining heroes, Lilliput starts to change colors and sneeze uncontrollably. Gosalyn gets the ray gun and as Lilliput sneezes, she uses it and un-shrinks Darkwing along with a couple of germs. Darkwing easily captures Lilliput.
Once back home, Darkwing is lying on the sofa. Turns out he was contagious and now everyone is sick.