Ellie Mae is first seen in her house at Devil's Bayou with her husband Luke, she is watching the sky and notices that her friend Orville is burning and urges Luke to wake up. They watch as Orville falls on a nearby pond with two passengers, Bernard and Miss Bianca. She quickly rushes to help Miss Bianca while Luke helps Bernard. They inform them that they are from New York, and soon they hear Medusa in her Swampmobile and Ellie Mae remarks that she would like to give Medusa a few whacks with her rolling pin. Then they see that Penny has been captured by Madame Medusa's pets Brutus and Nero.
Ellie Mae mentions with sadness "that poor little young'un tried to run away again" which means that the Swamp Folks know about Penny's capture and her escape attempts. Bernard and Bianca decide to follow Brutus and Nero, so Ellie Mae gets them to the boat of Evinrude. As the mice and Evinrude depart, she tells them that she will gather all the neighbors for help.
Later on in the film, Ellie Mae has gathered all the neighbors in her house: Deadeye, Gramps, Digger, and Deacon Owl; they are waiting for Evinrude's signal for the attack. When Evinrude finally arrives at Ellie Mae and Luke's house exhausted after being chased by hungry bats, Luke gives him a drop of his moonshine, and Evinrude regains his energy and calls everyone to attack. All of the Swamp Folks race to the riverboat where Medusa is holding Penny and Mr. Snoops.
Soon a fight starts and all of the Swamp Folks start attacking Medusa, with Ellie Mae uses her rolling pin as a weapon against Medusa (fulfilling her wish at last). The villainess manages to break free and starts shooting at the critters who then encounter Brutus and Nero, making the Swamp Folks run away with Ellie Mae going to the roof of the boat. When Medusa starts shooting at Penny (who is now trying to start the Swampmobile in order to escape) and is about to deliver a lethal shot at the girl after shooting out the Swampmobile's windshield, Ellie Mae jumps on her head and knocks her with her rolling pin. Medusa tries to shoot her but is foiled by Deacon Owl, who stuffs a dynamite stick in the gun, blowing it apart, removing Medusa's main option for fighting. As Penny and all of the critters try to start the Swampmobile, Bernard notices that there is no gas, so Ellie Mae makes Luke fill the gas tank with his moonshine.
As they manage to start the car, Medusa manages to make a grab on the Swampmobile, but Ellie Mae hits her in the hands with her rolling pin, making Medusa lose her balance, but the villainess grabs a rope and chases them like a water skier (later with her pet crocodiles). Fortunately, the rope is cut when Penny makes a turn on the Swampmobile to avoid running into the now sinking Riverboat, and Medusa is sent flying through the air into the Riverboat's smokestack. The group happily celebrate their victory and escape with Ellie Mae commenting that they gave Medusa what she deserved, After that she isn't seen again for the film.
Ellie Mae is not seen again for the end of the film, but it is also possible that she sent Evinrude with another message of help to the Rescue Aid Society, for Bernard and Miss Bianca.