In the Australian Outback, a young boy named Cody rescues and befriends a rare golden eagle called Marahute, who shows him her nest and eggs. Later, the boy is captured in an animal trap set by Percival C. McLeach, a local wanted poacher. When McLeach finds one of the eagle's feathers in the boy's backpack he is instantly overcome with excitement, for he knows that to capture such a grandiose bird would make him rich. McLeach kidnaps the boy and attempts to force out of him the whereabouts of the rare eagle.
Meanwhile, a message is sent to the Rescue Aid Society headquarters, and Bernard and 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 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 is the RAS' local regional operative. Jake later flirts with Bianca, much to Bernard's anger. He serves as their 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.
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 himself and the animals, but is thwarted by Joanna, McLeach's pet goanna. McLeach ultimately tricks Cody into thinking that someone else has shot Marahute, making Cody lead him to Marahute's nest.
Bernard, Bianca, and Jake, half-aware of what is happening, jump onto McLeach's Halftrack to follow him. At Marahute'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. Joanna tries to eat Marahute's eggs, but Bernard found the nest first and replaced the eggs with stones in order to protect them. Wilbur arrives at the nest, whereupon Bernard convinces him to sit on the eagle's eggs, so that Bernard can go after McLeach. McLeach takes Cody and Marahute to Crocodile Falls, where he ties Cody up and hangs him over a large group of crocodiles and attempts to feed him to them, but Bernard, riding a type of wild pig called a "Razorback", which he had tamed using a horse whispering technique earlier used by Jake, follows and disables McLeach's vehicle, preventing the use of its crane to put Cody at risk. McLeach then tries to shoot the rope holding Cody above the water. To save Cody, 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 reaches the shoreline, while McLeach goes over an enormous waterfall to his death.
Bernard dives into the water to save Cody, but fails. Jake and Bianca free Marahute in time for her to save Cody and Bernard, sparing them McLeach's fate. 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.