Looking up to the sound of frantic tweets and twitters, our heroes spot a lone Pidgey being attacked by a Fearow. Ash decides to help, sending out Noctowl to use Hypnosis. Seeing the illusion of a Charizard, the Fearow flees in terror. Despite Ash's efforts, however, the Pidgey collapses and falls down a nearby cliff. Noctowl flies down to save it, and when brought back up, Brock patches up its injured wing. Noticing that the Pidgey is sporting a cap and something on its back, the gang decides to go and find its trainer.
Arriving at a nearby town, Ash, Misty, and Brock notice dozens of similar Pidgey with objects strapped to their back. A young boy, Malachy, approaches and claims the Pidgey, whose name is Ken, as his grandfather's carrier Pidgey. He explains that his grandfather sends flocks of Pidgey to deliver packages and newspapers to all the nearby islands that don't have regular ferry services. Malachy adds that he wants to be a Pidgey Express Man someday as well.

Spying on our heroes from manhole not too far away, Team Rocket plans on stealing the carrier Pidgey in order to earn some extra cash. James wonders how catching all the Pidgey will be possible, but Meowth comes up with an idea.
Meanwhile, Malachy takes the gang to the Pidgey Express Building. Showing them the Pidgey Coop on the roof, our heroes find Malachy's grandfather as well. Malachy explains to him that Ash, Misty, and Brock saved Ken from the Fearow, so he thanks the gang for the favor and invites them inside for refreshments.
Inside, Ash inquires on how the Pidgey are able to find their way around the area. Malachy's grandfather explains that he takes the Pidgey on rides in a mini-blimp, showing them the routes repeatedly. Suddenly, Malachy decides to go check on the Pidgey and leaves the room. Ash mentions that Malachy would make a great Pidgey Express Man as he gets older, but Malachy's grandfather tells him that the Pidgey Express business is going to retire when he does. Shocked, Ash asks why. Malachy's grandfather replies that in today's world, it's hard to compete with airplanes and E-mail, and that it takes a life's dedication to run the business. He adds that he has missed a lot of things in his life, and he doesn't want the same to happen to Malachy.
As he's sweeping the coop, Malachy chats and plays with the Pidgey in the boxes. Looking on, Ash, Misty, and Brock begin to feel sorry for Malachy and the Pidgey when they hear that the business won't live on.
Still inside, Malachy's grandfather gets a call from the Pokémon Center in Way-Away Island, informing him that the Pidgey sent to deliver some medicine hasn't arrived yet. Worried, he takes out a pair of binoculars and surveys the landscape from the roof. Malachy and the gang arrive and wonders what's wrong. Malachy's grandfather explains the situation, and Malachy volunteers to find the lost Pidgey using the mini-blimp. Ash, Misty, and Brock decide to tag along as well. Malachy's grandfather tries to stop his grandson, but he ignores him and sets off on the rescue mission. Ash sends out Noctowl to help, and instructs Malachy to follow it.
Floating through the clouds nearby, Team Rocket spots another carrier Pidgey to steal. James pushes a button, and the Pidgey is sucked in a vacuum, winding up in a small bag with a couple dozen of other stolen Pidgey. Meowth looks around for more Pidgey, but instead finds the gang. Jessie and James prepares to run away, but Meowth reassures them that he came prepared for the situation. Pushing a button, smoke emerges from the balloon, and Team Rocket is concealed in an artificial cloud.
Noctowl and Ken spot the strange-looking cloud, and decide to fly over to investigate. The two Pokémon use their Gust attacks to blow the smoke away, and our heroes finally realize it's Team Rocket. Jessie and James perform their motto, coughing and wheezing their way through.
Misty spots the Pidgey in the bag, and Malachy demands for them to be returned. Jessie responds by sending out Arbok, forgetting that they're in midair, and that there's no ground to stand on. As Arbok prepares to plunge toward the Earth, Jessie, Wobbuffet, Meowth, and James grab onto its tail while it uses Poison Sting on Ken and Noctowl. Noctowl uses Hypnosis on Arbok and Team Rocket, making them attack an illusion of the gang's mini-blimp. While they're distracted, Noctowl and Ken try to rip the bag apart, and after several attempts, they're successful. The Hypnosis finally wears off, and Team Rocket realizes what has happened. Now facing a flock of Pidgey, Team Rocket tries to speed away. Pikachu stops them with Thunderbolt, and as they're left immobile, all the Pidgey and Noctowl peck holes in the balloon, sending them blasting off again.
On Way-Away Island, the medicine is finally delivered to the Pokémon Center. Joy thanks Malachy, and our heroes return to the Pidgey Express Building from which they came.
Malachy congratulates Ken for becoming a full-fledged member of the Pidgey Corp. After careful thought, Malachy's grandfather decides to consider letting Malachy take over the business, and all is well. Our heroes take their leave, continuing their way to Ecruteak City