In the Australian Outback, Cody, a young boy, wakes to the sound of a distant horn. He sneaks past his mother, eager to leave the house, but she calls to him, reminding him to be home for supper. Cody follows the call through the jungle to Faloo, a kangaroo. After Faloo urgently tells Cody that Marahute, the great golden eagle, is caught in a poacher's trap that only he can access, Faloo escorts Cody to the scene, and he makes a treacherous climb up a cliff. Although Marahute panics when she sees Cody’s knife, he is able to cut her free, but he is knocked off the cliff in the process. As he falls, Marahute flies below Cody, catches him on her back, and takes him on an exhilarating ride to her nest. When Cody learns the father of Marahute’s eggs is gone, he tells her that he has also lost his father. Giving Cody one of her yellow feathers, Marahute returns him to the jungle floor, where he unknowingly passes a “Wanted” poster for a man named McLeach and finds a mouse tied to a bell. As Cody sets the mouse free, he triggers a trap and falls into a trench. Receiving a signal from the trap, the poacher, McLeach, roars to the scene in his tractor with his pet goanna, Joanna. Realizing he has captured a boy instead of wildlife, McLeach denies his connection to the trap and blames Joanna for digging holes, but Cody is not deceived and indignantly tells him that poaching is illegal. McLeach then points his shotgun at Cody and uses it to pull him out of the trench. When Joanna sees the mouse in Cody’s knapsack and attacks, she knocks McLeach into his own trap. After angrily hoisting himself free, McLeach aims his gun at Joanna but notices Marahute’s feather attached to Cody’s knapsack. Tucking Marahute’s feather in his hat, McLeach asks Cody where he got it, but Cody tells McLeach it is a secret. The poacher then procures an identical feather from his vest, telling Cody that he already killed the father, and demands to know where the mother and her eggs are. Cody breaks free and runs, but is trapped by McLeach and Joanne at the edge of a cliff. Although Cody threatens that his mother will call the Rangers, McLeach is unfazed and drops Cody’s knapsack into the crocodile infested waters below, staging Cody’s death. As Cody is hauled off in a cage, the mouse scampers to the R.A.S. Telegraph Office to call for help. A Morse code signal reaches New York City, where delegates of the Rescue Aid Society are called to an emergency meeting. The moderator reports the kidnapping, but when he attempts to assign the case to the Society’s most prestigious members, he is shocked to find them missing. Bernard and Miss Bianca are instead dining at a fine restaurant, where Bernard nervously prepares to propose marriage, but he drops the ring before he can present it to her. When he returns to the table after retrieving the ring, Miss Bianca has received word of the kidnapping. Bernard misinterprets Miss Bianca’s willingness to perform the rescue mission and thinks she is referring to their marriage, so after rushing to the R.A.S. meeting, he is surprised when Miss Bianca announces that they are leaving on a delegation to Australia. At Albatross Air, Miss Bianca and Bernard meet Wilbur, a gawky seabird, who is unwilling to fly in the snowstorm until Miss Bianca tells him about the kidnapping. Back in Australia, McLeach takes Cody to his compound in the desert while Cody’s mother’s calls to her son go unanswered. Wilbur and the mice hitch a ride on an airplane, dive from the hatch in Sydney and make a bumpy landing in Mugwomp Flats, Australia. Jake, a kangaroo rat who operates the airport, is upset by Wilbur’s lack of concern for the incompatibility between his size and the runway, but he is charmed by Miss Bianca’s beauty and warmly welcomes the visitors. Wilbur, whose back is injured from the landing, is taken to a mouse hospital while Miss Bianca and Bernard leave on their mission, promising to return when they find the boy. Discovering that Miss Bianca and Bernard are unwed, and that they are looking for Cody, Jake offers to be their guide in hopes of getting closer to Miss Bianca. Meanwhile, McLeach interrogates Cody by calling out possible sites of Marahute’s nest while throwing knives at their locations on a map hanging behind Cody, but the boy insists he does not remember. Finally alone with Miss Bianca, Bernard attempts to propose again, but he is interrupted by Jake, who valiantly ropes an enormous snake and commands it to take them on their journey. Locked in a cage, Cody discovers he is in a dungeon inhabited by rare animals McLeach has caught but not yet killed. When Cody promises the animals that they will be released, Frank, a frill-necked lizard, suggests that they attempt to reach the keys hanging by the door. With the help of the animals, Cody extends the arm of a hook and secures the keys, but Joanne sticks her head through the door, destroys the hook and returns the keys to the wall. Undeterred, Frank uses his tail to pick the lock of the cage he shares with Cody. As Miss Bianca, Bernard and Jake proceed on their journey, now riding fireflies, Wilbur corrects his spine and eagerly leaves the hospital to find them. Meanwhile, Cody’s mother is presented with the remains of his knapsack that is recovered from Crocodile Falls, and the search is called off because Rangers assume Cody was the victim of a crocodile attack. Listening to the report on a radio, McLeach congratulates himself for outsmarting the authorities and realizes the best way to weaken Cody into revealing the location of Marahute’s nest is to threaten her eggs. Back in the dungeon, Frank releases the lock on his cage with his tail, but attracts the attention of Joanna as he noisily retrieves the keys. While Joanna chases Frank, Cody gets hold of the keys and releases himself, but the commotion draws McLeach and he takes Cody away from his new friends. When Miss Bianca, Bernard and Jake arrive at McLeach's compound, they see him free Cody. McLeach claims that Marahute has already been shot, but Jake warns it is a trick. As Cody walks away, McLeach baits him by telling Joanne that the eggs will never survive without their mother. Knowing that Cody will rescue the eggs, McLeach follows him in his tractor and Miss Bianca, Bernard and Jake climb aboard. At Marahute's nest, the mice warn Cody about McLeach as Marahute flys toward them. Although Cody yells at her to stay away, McLeach launches a missile at Marahute and she becomes ensnared in his trap. Capturing Marahute, Cody, Miss Bianca and Jake in this tractor’s cage, McLeach revels in the riches he will receive for trapping Marahute. McLeach then sends Joanna to eat the eggs, but Bernard has replaced them with rocks. Wilbur then arrives at the nest and Bernard talks him into sitting on the eggs while he rescues the others. Back at Crocodile Falls, McLeach dangles Cody over the water on a rope connected to his tractor, but the power suddenly goes out. After berating Joanna, McLeach notices his keys are missing. While Bernard sneaks away with the keys, he is spotted by Joanna. As she chases him, Bernard throws the keys to Bianca and Jake. McLeach shoots the rope holding Cody down to a thread, but as he aims to take his final shot, Bernard causes Joanna to crash into McLeach and watches them fall into the water. As the crocodiles divert their attention from Cody to McLeach, Joanna swims ashore and Cody’s rope breaks, sending him into the water. Jake and Miss Bianca attempt to unlock themselves from the cage while Bernard jumps into the water after Cody, grabs the rope and ties it around a branch. As the current grows stronger, the crocodiles retreat from McLeach, who assumes he has beaten them. However, McLeach soon realizes he is being pulled toward a waterfall and plunges to his death. Just as Jake opens the lock to the cage, Bernard’s branch breaks, sending Cody and Bernard over the waterfall. Freed from the cage, Marahute flies with Miss Bianca and Jake to save them. Soaring home on Marahute’s back, Cody thanks Bernard and Miss Bianca accepts Bernard’s marriage proposal. Back at Marahute’s nest, Wilbur calls for help and prepares to leave when the eggs hatch. As he coddles them, a baby chick greets Wilbur with a painful pinch.