In the stunning Outback, a young boy named Cody finds himself in a remarkable adventure when he rescues and befriends a rare golden eagle named Marahute. This majestic bird not only shows him her nest and eggs but also gifts him one of her precious feathers as a token of their bond. However, danger looms when Cody unwittingly falls into an animal trap set by the cunning poacher Percival C. McLeach, who is infamous for having killed Marahute's mate and is actively sought by the Australian Rangers. In a bid to save a mouse who has been used as bait, Cody finds himself in peril. Upon realizing that Cody possesses Marahute’s feather and quite possibly knows her location, McLeach decides to kidnap the boy, tossing his backpack into a float of crocodiles to make it seem as though Cody has met a gruesome fate.
The situation escalates as the courageous rescued mouse races to an RAS outpost to alert them about Cody's abduction. This prompts an urgent telegram to be dispatched to the Rescue Aid Society headquarters in New York City. Here, the esteemed agents, Bernard and Miss Bianca, are reluctantly pulled away from what was supposed to be a moment for Bernard to propose to Bianca. Their mission entails finding Orville, the albatross who previously assisted them, only to discover he has retired and his brother Wilbur has taken over the flying duties. Despite the bitter winter weather, Wilbur is determined to help them reach Australia, motivated by his disdain for child abduction. Upon arrival, they encounter Jake, a lively hopping mouse who serves as the local operative for RAS. Flirtatious and charming, Jake quickly finds himself smitten with Bianca, much to Bernard's concern. Consequently, Jake takes on the role of their "tour guide" while they search for Cody.
After a minor fiasco that results in Wilbur bending his spine while trying to assist, he ends up in a dilapidated ambulance. Although terrified of a surgery involving dangerous instruments, Wilbur bravely straightens his back and takes to the sky once again to find his friends. Meanwhile, at McLeach's hideout, Cody stands firm against the poacher, refusing to reveal Marahute's location. In a sinister ploy, McLeach deceives Cody into believing that Marahute has been harmed, knowing it will compel him to return to her nest.
Eventually, McLeach ensnares both Cody and Marahute, along with Jake and Bianca. However, in a twist of fate, Bernard manages to hide Marahute’s eggs from McLeach’s grasp. Taking his captives to the treacherous Crocodile Falls—a notorious waterfall where he previously discarded Cody's backpack—McLeach plots a horrifying end for Cody, intending to sacrifice him to the crocodiles lurking below. Just as hope seems lost, Bernard, now riding a razorback pig he has tamed using a horse whispering technique learned from Jake, arrives to thwart McLeach's villainous plan.
The chaotic climax ensues as McLeach tries to shoot the rope holding Cody above the ravenous crocodiles, but his scheme backfires when Bernard ingeniously tricks Joanna, McLeach's accomplice, into crashing into him. As the crocodiles turn on McLeach and Joanna, the situation spirals into chaos, leading McLeach to a desperate swim for the shore—that ends with him tumbling over the waterfall to a fitting demise. Bernard then jumps into the water, holding Cody long enough for Jake and Bianca to rescue Marahute, who swoops in just in time to save them both.
In the aftermath of their harrowing ordeal, Bernard finally musters the courage to propose to Bianca, who joyfully accepts his offer. Jake, observing their new bond, salutes Bernard with newfound admiration. With their adventure behind them, the group prepares to return home safely, unaware that Wilbur is still sitting on Marahute's eggs, which are about to hatch—leading to unexpected antics as one of the eaglets gives Wilbur a little bite, leaving him bewildered.
