In the Australian Outback, a young boy named Cody rescues and befriends a rare golden eagle called Marahuté, who shows him her nest and eggs. Later on, the boy falls in an animal trap set by Percival C. McLeach, a local poacher wanted by the Australian Rangers. When McLeach finds one of the eagle’s feathers on the boy’s backpack, he is instantly overcome with excitement, for he knows that catching an eagle that size would make him rich because he had caught one before, which was Marahuté’s mate. McLeach throws Cody’s backpack to a pack of crocodiles in order to trick the Rangers into thinking that Cody was eaten, and kidnaps him in an attempt to force him to reveal the whereabouts of Marahute.
A mouse, the bait in the trap, runs off to a secret outpost. From there, a telegram is sent to the Rescue Aid Society headquarters in New York, and Bernard and Miss Bianca, the RAS’ elite field agents, are assigned to the mission, interrupting Bernard’s attempt to propose marriage to Bianca. They go to find Orville the albatross who aided them previously, but instead find his brother Wilbur. Bernard and Bianca convince Wilbur to fly them to Australia to save Cody. In Australia, they meet Jake, a hopping mouse who is the RAS’ local regional operative. Jake becomes infatuated with Bianca and starts flirting with her, much to Bernard’s chagrin. He serves as their ”tour guide” and protector in search of the boy.
At the same time, Wilbur is immobilized when his spinal column is bent out of its natural shape, convincing Jake to send him to the hospital (an old abandoned ambulance). As Wilbur refuses to undergo surgery and flees, his back is unintentionally straightened by the efforts of the mouse medical staff to prevent him from escaping through a window. Cured, Wilbur 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 himself and the animals, but is thwarted by Joanna, McLeach’s pet goanna. Realizing that Marahute’s eggs are Cody’s weak spot, McLeach tricks Cody into thinking that someone else has shot Marahute, making Cody lead him to Marahute’s nest.
Bernard, Bianca, and Jake, knowing that Cody is in great danger, jump onto McLeach’s Halftrack to follow him. At Marahuté’s nest, the three mice try to warn Cody that he has been followed; just as they do, McLeach arrives and captures Marahute, along with Cody, Jake, and Bianca. On McLeach’s orders, Joanna tries to eat Marahuté’s eggs, but discovers that they are just egg-shaped stones. Frightened that McLeach might be angry with her, Joanna drops the stones over the cliff. When she leaves, Bernard crawls out of the nest with the hidden eggs, grateful that Joanna fell for the trick. Wilbur arrives at the nest, whereupon Bernard convinces him to sit on the eagle’s eggs, so that Bernard can go after McLeach. Infuriated by Cody’s interference, McLeach takes his captives to Crocodile Falls, where he ties Cody up and hangs him over a group of crocodiles in attempts to feed him to them. But Bernard, riding a wild razorback pig, which he had tamed using a horse whispering technique used by Jake on a snake earlier, follows and disables McLeach’s vehicle.
McLeach then tries to shoot the rope holding Cody above the water. To save Cody, Bernard tricks Joanna into crashing into McLeach, sending both of them into the water. The crocodiles then turn their attention from Cody to McLeach and Joanna, while behind them the damaged rope holding Cody breaks apart. McLeach fights and fends off the crocodiles, but while Joanna reaches the shoreline, McLeach is swept over the waterfall to his death. Bernard dives into the water to save Cody, but fails. His actions, however, buy Jake and Bianca enough time to free Marahuté for her to save both Cody and Bernard.
Bernard, desperate to prevent any further incidents, proposes to Bianca, who eagerly and happily accepts while Jake salutes him with a new-found respect. All of them depart for Cody’s home. Meanwhile, Marahute’s eggs finally hatch, much to Wilbur’s dismay.