Captain Jake and the Never Land Pirates Joins The Rescuers

In an abandoned river boat in Devil's Bayou, a young orphan named Penny drops a message in a bottle, containing a plea for help into the river. The bottle washes up in New York City, where it is found by the Rescue Aid Society, an international mouse organization inside the United Nations. The Hungarian representative, Miss Bianca, volunteers to accept the case and chooses Bernard, a stammering janitor, as her co-agent. The two visit Morningside Orphanage, where Penny lived, and meet an old cat named Rufus. He tells them about a woman named Madame Medusa who once tried to lure Penny into her car and may have succeeded in abducting Penny this time.

The mice travel to Medusa's pawn shop, where they discover that she and her partner, Mr. Snoops, are on a quest to find the world's largest diamond, the Devil's Eye. The mice learn that Medusa and Mr. Snoops are currently at the Devil's Bayou with Penny, whom they have indeed kidnapped and placed under the guard of two trained alligators, Brutus and Nero. With the help of an albatross named Orville and a dragonfly named Evinrude, the mice follow Medusa to the bayou. There, they learn that Medusa plans to force Penny to enter a small hole that leads down into a pirates' cave where the Devil's Eye is located.

Bernard and Miss Bianca find Penny and devise a plan of escape. They send Evinrude to alert the local animals, who loathe Medusa, but Evinrude is delayed when he is forced to take shelter from a flock of bats. The following morning, Medusa and Mr. Snoops send Penny down into the cave to find the gem. Unbeknownst to Medusa, Miss Bianca and Bernard are hiding in Penny's skirt pocket. The three soon find the Devil's Eye within a pirate skull. As Penny pries the mouth open with a sword, the mice push it out from within, but soon the oceanic tide rises and floods the cave. The three barely manage to retrieve the diamond and escape.

Medusa breaks her promise to Snoops that he can have half the diamond, and hides it in Penny's teddy bear while holding Penny and Snoops at gunpoint. When she trips over a cable set as a trap by Bernard and Bianca, Medusa loses the bear to Penny, who runs away with it. The local animals arrive at the riverboat and aid Bernard and Bianca in trapping Brutus and Nero, then set off Snoops's fireworks to create more chaos. Meanwhile, Penny and the mice commandeer Medusa's swamp-mobile, a makeshift airboat. Medusa unsuccessfully pursues them, using Brutus and Nero as water-skis, and is left clinging to the boat's smoke stacks as Snoops escapes on a raft and laughs at Medusa, while the irritated Brutus and Nero turn on her and circle below.

Back in New York, the Rescue Aid Society watch a news report of how Penny found the Devil's Eye, which has been given to the Smithsonian Institution, and how she has been adopted. The meeting is interrupted when Evinrude arrives with a call for help, sending Bernard and Bianca on a new adventure.