Chris and Big are still looking for Froggy, when Chris spots the X Tornado flying overhead and wonders if Tails is okay. When they find Froggy, the frog gets caught into the trap that sets an alarm. McLeach shows up with Cody as hostile and steals Froggy. Chris and Big go after McLeach on to an Abandoned Opal Mine.
Meanwhile, a message is sent to New York 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 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 ultimately 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 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 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. Budgie and Zak free the animals with the help of Sonic and Tails. McLeach takes Cody and Marahute to Crocodile Falls, where he ties Cody up and hangs him over the eponymous crocodiles. 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 a much larger waterfall to his death.
Bernard dives into the water to save Cody, but fails. Jake and Bianca free Marahute in time for her to 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.
Just then, Omega arrives and steals Froggy. Eggman tells Decoe and Bocoe to bring the Egg Carrier down to pick up Omega. Eggman unleashes his Egg Genesis robot on them, which Sonic and Silver defeat. Sonic and Tails take off in the Tornado-1 to go after the Eggman Craft 3 to save Chocola and Froggy. Later, Chris and Big head on McLeach's vehicle to Mount Warning. Silver sees Hexxus on the leveler, but moments after he left, Chris spots the White Chaos Emerald in the Leveler and rushes off to give it to Silver.
- When McLeach goes over an enormous waterfall to his death, he screams the Howie Scream.
- Zak stows away in Budgie's pocket.
- Unlike the The Rescuers Down Under, Red, Frank and Krebbs are now saved.