Ash and his friends are making their way to Ecruteak City when they encounter a Pidgey that is being attacked by a massive Fearow and decide to intervene. Ash sends out Noctowl to battle Fearow, and it hits it with Hypnosis. Now convinced that Noctowl is a Charizard, Fearow flees the battle. However, Pidgey has become too exhausted to stay in midair and starts falling. As it had flown even further away from them during the battle, the group can only watch as it tumbles through the air and out of sight beyond the treetops.
With Noctowl flying ahead of them, the three friends break into a sprint that takes them through the trees and to edge of a steep drop-off where they discover that the tiny bird's free-fall has come to an abrupt end. Pidgey has crash-landed on a rocky outcrop protruding from the sheer face of a small cliff! Ash orders Noctowl to retrieve it, but Pidgey is understandably terrified when Noctowl lands beside it and begins to struggle feebly. Noctowl once again uses its Hypnosis, this time making itself appear as a fellow Pidgey.
Having retrieved the tiny Pidgey, Brock carefully ties a bandage to Pidgey's broken wings. Misty notices the backpack on Pidgey, while Ash suggests taking the tiny bird in order to find its Trainer. They quickly arrive in town, and while walking along the pavement, they notice a flock of Pidgey flying around town with the same backpack as the Pidgey they found. Then, a young boy named Malachi runs towards them, recognizing the Pidgey, whose name is revealed to be Ken. Seeing the bandage on Ken's wings, Malachi accuses them of hurting his Pidgey, but Brock quickly calms him saying they only helped it after its encounter with the Fearow, followed by Malachi's apology.
Next, Ash congratulates him for its Pidgey, but Malachi explains the little Pidgey is one of his grandfather's carrier Pidgey which delivers letters and newspapers to the islands nearby. From a close sewer, a camera is seen spying on them. As the camera turns to the inside of the sewer, Team Rocket is seen making a plot in order to steal every carrier Pidgey. The scene then reverts to the others who have arrived at the Pidgey Express building. Malachi takes them to a coop full of Pidgey where his grandfather gives instructions to four of them, which are preparing to make a delivery.
After becoming acquainted with Ash, Misty, and Brock, he invites them inside for some refreshments in order to express his gratitude for saving his Pidgey. After explaining his methods of training, his grandson Malachi goes back to the coop in order to spend time with the Pidgey. After he left, Ash notices his strong love for the Express. Malachi's grandfather agrees, informing them after his retirement the business will be closed. He then proceeds to explain his reasons which include the inability of competing with airplanes and e-mail, and the fact that it takes a whole life to dedicate.
Later, Malachi's grandfather answers a call from Nurse Joy who informs him about the absence of the Pidgey which was supposed to deliver some medicine. He rushes with his binoculars to scout the sky in hopes of seeing the wayward Pidgey. The others notice him and found out about the missing Pidgey, to which Malachi reacts by saying he is going to find the Pidgey using the blimp which his grandfather uses to train them. Ash and the rest offered to go, and they all lift-off in search of the Pidgey.
Ash sends out his Noctowl to scout the area and the scene turns to Team Rocket's balloon having attached underneath it a retriever system with a bag full of Pidgey. After stealing another Pidgey, Jessie notices the blimp searching for the Pidgey. In order to avoid being seen by them, Meowth activates a button that engulfs the entire balloon into white smoke making it appear as a cloud. But their scheme is quickly discovered by Noctowl which uses Whirlwind to blow away the smoke.
After the two sides encounter, Jessie sends her Arbok. Realizing it's floating in the air, it almost falls when it is quickly grabbed by Team Rocket by its tail. While hanging, it uses Poison Sting to attack Ken and Noctowl. Noctowl dodges then uses Hypnosis to trick Arbok into thinking he attacks the others, while actually missing. Then, Noctowl and Ken tear the bag, releasing the Pidgey. When Team Rocket finally snaps out of Hypnosis, the Pidgey are all released while soaring the sky.
When they realize they are surrounded, Team Rocket proceeds to flee but are quickly shocked by Pikachu's Thunderbolt. Then, the flock of Pidgey peck their balloon, blowing it up and sending them blasting off. Next, Ash along with the others, successfully deliver the medicine to Nurse Joy and return to the Pidgey Express. Back to the rooftop, Malachi is waiting for the arrival of Ken, which successfully made his delivery.
Malachi's grandfather reveals that he changed his mind about closing the Express by informing Malachi the family business will be run by him after his retirement if he proves to be a professional. Ash then congratulates Malachi and the scene cuts to the group bidding farewell.