A team of over 415 artists and technicians were required for the production of the film. Five members of the team traveled to the Australian Outback to observe, take photographs and draw sketches to properly illustrate the outback on film.
On its initial release, The Rescuers Down Under was preceded by a short subject starring Mickey Mouse in an adaptation of The Prince and the Pauper. (This was only the second new Mickey Mouse short made since the 1950s, the first being Mickey's Christmas Carol, which was made to accompany the 1983 re-release of The Rescuers.)
The movie starts with Cody, a young boy from the Outback, who hears a distress call that leads him to find a giant great golden eagle named Marahute in a rope trap on top of a cliff. After Cody frees the eagle, he accidentally is knocked off the cliff. Marahute catches him at the last moment and gives him a ride on her back. After she shows him her eggs and gives him a feather as thanks for saving her, Cody sets off for home. On the way, he stumbles into a poacher's trap set by Percival McLeach. McLeach realizes that Cody knows Marahute's location and kidnaps the boy, intending to capture the bird and sell her.
Bernard and Bianca, the protagonists of the original The Rescuers film, receive word from the Rescue Aid Society of Cody's kidnapping. They go to find Orville the albatross who aided them previously, but instead find Wilbur, Orville's brother. Bernard and Bianca convince Wilbur to fly them to Australia to save Cody. In Australia, they meet Jake, a kangaroo rat, who flirts with Bianca, much to Bernard's chagrin. He serves as their guide and protector in search of the boy. Wilbur is immobilized when his spinal column is bent out of its natural shape, convincing Jake to consign him to hospital. When he refuses to undergo surgery and instead attempts to flee, Wilbur's back is unintentionally straightened by the efforts of the mouse medical staff to prevent him escaping through a window. Cured, he departs in search of his friends.
At McLeach's ranch, Cody has been thrown into a cage with several of McLeach's captured animals after refusing to give up Marahute's whereabouts. Cody tries to free the animals, but is thwarted by Joanna (McLeach's pet goanna). McLeach tells Cody that someone else has shot Marahute, tricking Cody into leading him to Marahute's nest. Bernard, Bianca, and Jake, half-aware of what is happening, jump onto McLeach's Halftrack.
At Marahute's nest, the three mice try to warn Cody that he has been followed; just as they do, McLeach arrives and captures Cody, along with Marahute, Jake, and Bianca. Wilbur arrives at the nest, whereupon Bernard convinces him to sit on the eagle's eggs, which Bernard had saved from Joanna moments before. McLeach takes Cody and Marahute to Crocodile Falls, where he ties Cody up and hangs him over the crocodiles. Bernard, atop a type of wild pig called a "razorback", which he had tamed using a technique earlier used by Jake, follows and disables McLeach's vehicle. McLeach then tries to shoot the rope holding Cody above the water. Bernard tricks Joanna into crashing into McLeach, sending them both into the water. The crocodiles chase McLeach, while behind them the damaged rope holding Cody breaks apart. Although McLeach manages to fight off the crocodiles, only Joanna makes it to the shore while McLeach falls off the waterfall.
Bernard dives into the water to try to save Cody, but fails. Jake and Bianca free Marahute just in time for her to burst free and retrieve Cody and Bernard. Bernard, desperate to avoid any further incidents, proposes to marry Bianca, who accepts eagerly while Jake salutes him with a newfound respect. All of them depart for Cody's home. Wilbur, whom they have neglected to relieve of his task, incubates the eggs until they hatch - much to his dismay.
The Rescuers Down Under features three characters from the first film: Bianca, Bernard, and the Chairmouse.
The Rescuers Down Under is sometimes considered the black sheep of the Disney Renaissance era (1989-1999) because of its poor box-office performance as well as its lack of musical numbers, ironic given the success of the original The Rescuers and despite its reasonable critical reviews. However, despite its poor reception, a third movie was later planned for 1996 (presumably due to its successful home video release), but Eva Gabor suddenly died the previous year from respiratory failure from complications of food poisoning. Therefore, the planned movie and all future Rescuers sequels were scrapped.