Bushroot is in his cell begging to get out and the guard walks off. Just then a bright light appears at Bushroot's cell window.
Darkwing and Launchpad are called to the prison. It seems that Bushroot is staring out the window and hasn't moved for two weeks. Darkwing thinks that Bushroot is dead, but Launchpad tries using his psychic powers to check his aura and trips over a vine that goes out the window. It seems that Bushroot was able to escape that way.
Back at home, Launchpad is using a pyramid hat to boost his psychic powers. Honker comes over and tells them that his parents are missing. They go over to the Muddlefoot's house and find dirt everywhere and a giant cabbage. They also find a tape in the VCR that tells how to care for the cabbage. On closer inspection, Darkwing spots Bushroot in the backgroud. They find out that the tape originated in a town called Twin Beaks.
The scene cuts to the town of Twin Beaks. Binkie is in a diner enjoying coffee being served by her twin (actually her sister Trudi) with an eye patch. Most of the other people are out working the fields, including Herb, and growing more of the large cabbage. Darkwing, Launchpad, Gosalyn, and Honker fly in on the Thunderquack and Launchpad puts on a blindfold to use his psychic powers to land the plane. He makes a good landing, but they are high up in the trees. As they are walking to town, Launchpad walks off in another direction to a field with cows. They wonder what he's doing and launchpad says that "The cows are not what they seem" and says the town is not far away and they should stop at Trudi's Diner. He tells them that the log he is carrying is telling him this. They go to the diner and they see the large cabbages everywhere being treated as if they were people. Darkwing is certain Bushroot is behind it all and Launchpad says the log doesn't think so. Binkie's sister comes to the table and tells Honker that his parents are outside helping with the "harvest". Honker greets his parents who are carrying a giant cabbage. He is glad to see him and they tell him that they couldn't have a harvest without him and Honker sees his twin pop out of the cabbage.
While Darkwing, Gosalyn, and Launchpad are in the diner discussing how strange things are, Launchpad mentions cows and everyone screams and runs out of the diner. They leave and go walking in the woods as the log has suggested. They come across what looks like another dead Bushroot wrapped in a plastic bag. Gosalyn goes off to find Honker. She finds him and he is holding a giant cabbage. Then she hears the real Honker telling her to watch out. Just then another Gosalyn pops out of the cabbage and grabs her. She throws them into the fake Herb and Binkie and grabs the real Honker and runs. They get to a dead end with the plant clones chasing them and a bright light appears.
Darkwing thinks that he will use his subconscious mind to solve the mystery and puts on a blindfold and runs right into a tree knocking him out. He has a strange dream about the cows, the cabbage, Bushroot, and the Muddlefoots. He wakes up and doesn't think that was any help. He talks to Gosalyn and mentions the cows and Gosalyn points to a talking cow with a space helmet.
Gosalyn explains that the cabbages are aliens that have come to their planet to take over and the cow is an alien that is here to stop them. The cow tells them that Bushroot was spying for them. The log that Launchpad is holding jumps out of his and and grows into Bushroot. It seems that Bushroot is helping defeat the alien cabbage menace. The cow tells them they need to delay the cabbages while she gets reinforcements on the way.
Darkwing, Bushroot, Launchpad, Gosalyn, and Honker are able to cause mayhem and stop the cabbages from shipping out the new crop and think they have won until the cabbages start sprouting Darkwings. Just when things were looking grim, the cow alien reinforcements arrive and start zapping the cabbages.
As the cows take away all the cabbages, Bushroot sneaks out with one and thinks that now he won't be the only mutant plant.
Trudi's Diner is a reference to the Double R Diner and Trudi herself is designed after Nadine Hurley.
The discovery of the second fake Bushroot corpse is akin to the discovery of Laura Palmer's body. Both corpses are wrapped up in plastic and Launchpad mimics a quote from Twin Peaks with the line: "It's Bushroot, he's dead!". Darkwing follows up on this with "wrapped up in plastic," as the original line goes: "She's dead, wrapped in plastic!".
"The cows are not what they seem," is based on "the owls are not what they seem,", spoken by the Giant.
The plot of the episode is inspired by the 1955 novel The Body Snatchers, which by 1992 was turned into a movie twice: once in 1956 and once in 1978.
Honker's shirt inexplicably is blue when Drake starts talking about the Muddlefoot's weirdness.