The series opens with Don Karnage and his band of Air Pirates hijacking and boarding a plane owned by Shere Khan to steal a box containing something that the pirates want. But just as Karnage and his men have returned with the box to their mothership, the Iron Vulture, a young bear cub named Kit Cloudkicker swipes it and then leads the pirates through a chase sequence that results in him jumping off the ship and sky-surfing out of there with his trusty air-foil, hitching a ride over to a tavern owned by King Louie, wherein he hides the box. Karnage and his boys bust in, and Kit annoys them some more before following customer Baloo, who allows him a ride in his cargo plane, which he calls the Sea Duck. The Air Pirates give chase, with Baloo not understanding why they're after him, but he manages to elude them by flying to the city of Cape Suzette, which the Air Pirates can't enter because the people working the cliff guns defending the entrance to the city keep shooting at them.
Having eluded the pirates, Baloo takes Kit to his "company building", actually a shack he likes to call Baloo's Air Service, which is in trouble because he never bothers paying his overdue bills. Baloo believes that he only works when he has to, and he considers making Kit his navigator. Kit explains that he has to get back to Louie's, but Baloo isn't in the mood to go back to the bar so soon. Then a man from the Cape Suzette National Bank shows up to tell Baloo that since he's so far behind on his bills, his plane is going to be repossessed. Baloo isn't at all happy about that, so he takes Kit's idea of taking a $3,000 job, promising that he'll take him to Louie's tomorrow if he helps him. But the job he takes is zoo delivery for gorilla-birds, the hardest ostriches one could attempt to control. As they're struggling to deliver the gorilla-birds, the Air Pirates show up again, this time causing Baloo to come in for a rough landing. At this point, Baloo realizes the pirates are after Kit and demands to know what the pirates want with him, and Kit reacts by storming off. Then Baloo discovers the gorilla-birds have run off.
Kit goes hacking through the jungle, only to be captured by Karnage, who ties him upside-down to a tree, demanding to know where the box is. Baloo has, in the meantime, gone looking for the gorilla-birds, and just when he's caught them all, he overhears Karnage tormenting Kit. To rescue him, he reluctantly lets the gorilla-birds loose and has them distract the pirates while he saves Kit. They make their way over a pack of alligators to get back to the Sea Duck and take off. As they fly off, Kit admits that he's hidden a big jewel at Louie's, and Baloo realizes with a jewel like that, he could buy back the Sea Duck.
The next morning, Baloo and Kit meet their service's new owner, Rebecca Cunningham, who says she's going to turn this failing business into a real moneymaker. Rebecca says that Baloo will have to pay her $50,000 to reclaim the Sea Duck, but until then, he's her staff pilot. Baloo agrees to this, because he can get to Louie's this way. Afterwards, Rebecca has the place's name changed to "Higher for Hire" and makes Baloo and Kit wear silly uniforms and the Sea Duck wear a clowny paint job. She then sends Baloo and Kit to go deliver mangos, but no sooner do they get out of her eyesight, they ditch their uniforms and try to head off for Louie's. But her daughter Molly, has stowed away, and she's willing to tell her mom if they don't allow her to come along. So they go ahead and bring Molly with them to Louie's.
Once there, Baloo and Kit find the jewel, but Louie tells them it isn't a jewel, and therefore is worthless. But when Kit mentions that Don Karnage had stolen it from Shere Khan, Baloo takes another look at it, only to have it shock him, making him decide that "maybe this night-light is worth something after all." But just as they're leaving, the Air Pirates come back to attack. After a lengthy chase sequence, Baloo and Kit manage to throw the pirates off course by dumping the mangoes on them. But when they return to Higher For Hire, Rebecca is furious that they jettisoned the cargo and doesn't believe that it was because they were attacked by pirates until Molly sticks up for them.
The next morning, before paying a visit to Khan Industries, Baloo and Kit hide the jewel in Molly's doll, Lucy, figuring that it would be wiser to find out how much Shere Khan is paying for its return before they actually do that. The jewel, Khan explains, is actually an electrical alloy developed by his scientists that is powerful enough to run his entire corporation, and he's offering them $100,000 for its return. But unbeknownst to either of them, Don Karnage snuck into Cape Suzette the previous night, accompanied by Dumptruck and Maddog, avoiding the cliff gun defenses, looking for Baloo's plane. When Baloo and Kit return to Higher For Hire, they find that the pirates have ransacked the place and kidnapped Rebecca and Molly, leaving behind a ransom note demanding they be given the stone.
Kit feels it's his own fault for the kidnapping, and as he helps Baloo find his way to Pirate Island, he confesses the story of his past. Until recently, he was an Air Pirate himself, but after about a year with Karnage and his men, he got sick of it and rebelled against them when he took the electrical stone. Baloo sympathizes for him. While that's going on, Karnage and his men hijack another of Shere Khan's planes, but they only steal seemingly useless stuff.
As Baloo and Kit land in the volcanic Pirate Island, Rebecca seduces the prison guard into letting them out by saying she'll give him ownership of the Sea Duck if he promises to let them go free. The guard agrees to this, but just as he gets the keys, Baloo knocks him out and takes the deed, then lets Rebecca and Molly out. Just then, Karnage and his men return and the good guys are forced to hide from the pirates' eyesight. Upon his return, Karnage reveals the master weapon he's been working on using the junk they've stolen- the Lightning Gun, with which, he says, they will use to plunder Cape Suzette. He then sings a catchy song about what he and his men are, during which the good guys try to sneak past disguised as other pirates, only to have Baloo stupidly join in the song, blowing their cover. To cover their escape, Kit pretends to rejoin the pirates and gives them the rock, but his acting angers Baloo, who ends up taking it too seriously. Baloo and the girls make their escape, not knowing that Kit was faking, but the bad guys are right behind. With the pirates unshakable, Baloo turns on an Overdrive function that allows them to get away very quickly, even though he warned it could destroy the Sea Duck's engines if used for too long.
Upon returning to Cape Suzette, they're suddenly snatched by Shere Khan's men, who bring them to the big tiger himself. Rebecca has no clue about this stone that everyone's talking about, so Khan has Dr. Debolt explain it: the "stone" is a kind of miniature nuclear reactor, a one-of-a-kind fluke creation that can generate limitless energy. Khan chastises Baloo for not retrieving the stone as promised, and the bear responds by complaining about everyone he's in the room with. Back at Higher For Hire, Baloo packs his bags into the Sea Duck and pays Becky for it in the form of gold dust he swiped from the pirates earlier. Rebecca and Molly, though, don't want him to leave, because they don't believe Kit's really gone bad.
Karnage and company load the Lightning Gun onto the Iron Vulture and make their way towards Cape Suzette. Over in the city, Rebecca goes looking for new cargo pilots and planes. Not far away, Dr. Debolt informs Shere Khan of Karnage's new Lightning Gun, but Khan doesn't believe it until he sees an explosion coming from the cliff guns and realizes that if the cliff guns have been destroyed, Cape Suzette is defenseless from invasion by Khan's Air Pirates. He calls up the air field to combat this menace, but they are no match for the machine.
Up on the Iron Vulture, Karnage announces to the citizens that he and his men are now going to plunder the city. But then, Kit snatches the stone and runs off with it, hiding in a radio room. There, he calls a Mayday to nearby pilots who aren't getting toasted to let Baloo know that he never really double-crossed him. Over at Louie's, Baloo is enjoying himself when a pilot runs in telling him that he's got a message from "Little Britches." When Baloo hears Kit's message over Louie's transmission radio, he realizes he was wrong and that Kit never betrayed him, so he jumps back into the Sea Duck and activates the Sea Duck's Overdrive again.
Back on the Iron Vulture, Kit tries to escape on his air-foil again, only to be snatched up by Dumptruck and have his "interesting toy" broken by Karnage. Karnage, furious that Kit lied to him, orders Dumptruck to drop Kit over the edge, but Baloo comes to the rescue just in time, burning out his Overdrive in the process. They hide under a bridge in order to deter Karnage from looking for them. Afterwards, Baloo radios Higher For Hire to say they're coming back. In spite of Baloo's suggestions, Rebecca refuses to leave the currently-being-fried city, and then states that she knows how to combat Karnage's Lightning Gun - coat the Sea Duck with an armor of rubber materials. After doing this, she joins Baloo and Kit for the ride, because they have armored the plane with her tires. When Karnage hears Baloo and Kit taunting him on his radio, he orders his men to try and blow them up, but just as specified, the rubberized Sea Duck is unaffected by the Lightning Gun. Karnage tries sending his men to chase the Sea Duck, but they all end up getting lost along the way. Baloo then reluctantly drives the Sea Duck right into the Lightning Gun, sending it crashing into the sea. Believing Baloo to be dead and with the pirates' weapon destroyed, Shere Khan orders the remnants of his air force to attack the Air Pirates, forcing Don Karnage and his gang to retreat in defeat before the Iron Vulture is overrun by Khan's fighters.
A week later, the Sea Duck is recovered and fully repaired, but since Rebecca paid for its repairs, she owns it again, so now Baloo is still stuck as her staff pilot. Only this time, he accepts the job, saying it's only until he's able to buy it back again. The whole group takes an enjoyable flight to the skies in the new Sea Duck, celebrating their new lives together.
When the film was cut up into syndicated reruns, several short scenes were cut out for time. Unfortunately, like with the Darkwing Duck pilot, these scenes were not restored when the pilot was released onto DVD in August 2006. However, most of these edited scenes do appear in the four-issue comic book adaptation put out by Disney Comics. Among the scenes that were cut:
- After answering the door when we first meet Rebecca, Baloo pulls out a "Gone Fishing" sign.
- When he breaks into Louie's, Karnage sees a drink on the table, downs it, and complements, "You always serve such tasty drinks, Louie!"
- When Louie walks up to Karnage, the pirate shoves his sword in his face. This edit is made obvious by the jump in the soundtrack.
- When discussing the job of delivering gorilla-birds, Baloo offers to take Kit to Louie's tomorrow if he'll help him.
- After Kit apologizes, "I'm sorry about your plane", Baloo replies, "Hey, don't worry - ya win some, ya lose some."
- When meeting Molly, Louie comments, "My my my, Baloo, these stewardesses are getting younger and prettier every day!"
- When telling Baloo that Karnage stole the rock, Kit says, "Yeah - Karnage lifted it from one of Shere Khan's planes."
- Near the end of part two, Rebecca sang a lullaby to Molly titled "Home is Where the Heart Is", all the while Kit eavesdrops and sympathizes. Although this scene was cut from syndication, an extended version of the song appears on the Disney Afternoon soundtrack.
- As Baloo and Kit leave his office, Shere Khan comments that "[the stone is] worth 50 times that."
- At the end of his message to Baloo, Kit whispers, "Always," emphasizing the fact that he's letting Baloo know he never betrayed him.