Ash is traveling through the forest on his way to Oreburgh City, where he hopes to earn his first Gym Badge in Sinnoh. But first he's helping Starly practice using Aerial Ace, a process that doesn't go entirely smoothly. Our heroes also catch the attention of Rosebay, a woman who monitors the Pokémon that live in the forest. Lots of Pokémon have been disappearing lately and she's not sure why, but it doesn't take long for Ash and his friends to decide they should help her out!
Meanwhile, Team Rocket have set up a trap in the Valley Path, an area which Flying-type Pokémon often pass through. All it takes some netting and soon Team Rocket is happily snagging lots of avian Pokémon for their Boss. When Ash sends Starly out to look for clues, Starly is swept up by Team Rocket's criminal plans as well—but Starly isn't about to sit back and wait to be rescued! Jessie and James leave Meowth to guard their ill-gotten Pokémon, and Starly is ready to stage a jailbreak together with help from a captured Hoothoot.
Hoothoot hypnotizes Meowth into letting the Pokémon go, but when Meowth snaps out of its trance, it calls for backup from Team Rocket's other Pokémon. However, Ash and his friends came across a Pidgeot trapped in Team Rocket's net and realized what was going on, and they show up looking for Starly! Jessie and James return and try to stop our heroes, only to discover that Brock's Bonsly can use Mimic to send their Pokémon's moves right back at them. Then Starly evolves into Staravia and pulls off a terrific Aerial Ace—which is also the term that describes Team Rocket as they go blasting off again. The trapped Pokémon are freed, Rosebay is happy, and now it's onward to Oreburgh City!
Ash is in the midst of some special training with Starly. He orders an Aerial Ace, and Starly does so, flying along the ground towards a target on a tree trunk. Ash tells him to pull up, and he flies up the trunk of the tree, before looping around for another go. However, this time Aerial Ace fails, and Starly crash-lands, injuring his leg. The group rushes over to Starly, and Brock says that it is just a minor injury, proceeding to treat him with a spritz of Potion and a bandage. Ash comments that they still need to do some more practice on Aerial Ace.
A nearby bush rustles and a girl steps out of it. She introduces herself as Rosebay. Brock is immediately infatuated, but Croagunk uses Poison Jabs to stop his flirting. Rosebay reveals that she is observing the Pokémon in the forest, and invites the group to join her. Rosebay then shows them a Swablu nest, but the nest is oddly empty. So Rosebay leads the group to higher ground, before commenting that the Swablu should have returned to the nest by that time. She also mentions that the bird Pokémon population has recently been shrinking, so the group offers to help her solve the mystery. Their search reveals that a local Hoothoot colony is strangely absent. Meanwhile in a nearby pass, Team Rocket’s gigantic net trap captures a flock of migrating Taillow and Swellow. Meowth and his teammates marvel at their success, and plan on handing some of the bird Pokémon over to Giovanni. While aiding the search effort, Ash’s Starly soon joins the caged Pokémon. Ash begins to worry about Starly, as he has been gone a long time. Rosebay realizes that all the bird Pokémon use the valley path, so that must be where they are. The group decides to hurry there as Starly might be in trouble.
Inside Team Rocket's secret base, Meowth reports back to Jessie and James, who ask him to sort out their gift for the boss. Meowth insists on a 'vote', so the group plays Rock Paper Scissors. Meowth loses, and gloomily asks what the others will be doing, but is disappointed to see his teammates relaxing in the sun. Up on the edge of the valley, the group spots Team Rocket, and Rosebay notices a Pidgeot in Team Rocket's net. Ash tells Pikachu to help it. Pikachu runs off and frees it from the net just as it is closing. Ash then orders Pikachu and Pidgeot to gather as many bird Pokémon as they can find, in order to tear down the net. The rest of the group runs off to free the Pokémon Team Rocket has already captured.
While Carnivine, Cacnea and Seviper guard the door to the cage room, Meowth walks in and puts a ring around a Swablu, immobilizing it. Starly and Hoothoot signal each other, and Hoothoot uses Hypnosis on Meowth; he releases Swablu. Now under control, Meowth promptly frees the Swablu and unlocks the cages. He reveals that they will need to dig a hole upwards to escape, so he lends his claws to aid their effort. Jessie and James are too relaxed to notice Rosebay and the group sneak into their base of operations. However, the crowds of dozens of bird Pokémon approaching disturbs their sunbathing. Pikachu orders his winged recruits to destroy the net trap. The group, still underground, watches on the security camera screens. Jessie and James rush to some controls, wondering where Meowth is. In the cage room Meowth and Starly are watching as all the other Pokémon leave through the escape tunnel, with Hoothoot leaving last. As Meowth snaps out of the Hypnosis, he calls in Seviper, Cacnea and Carnivine. They surround Starly, as the group runs into the room.
The ground starts to shake as Team Rocket's mecha rises from the ground. A ladder drops down, and Team Rocket's Pokémon climb the ladder into the mecha. Meowth apologizes, admitting to Jessie and James that he was Hypnotized to free the Pokémon. Jessie pushes a button, and nets pop out of the mecha's arms. The Pokémon flee out of the escape tunnel, with the group following behind. Ash yells for Pikachu to use Thunderbolt, but it doesn't affect the mecha, which is made of wood. Team Rocket then tries to stomp on the group with their mecha, but the force causes the ground underneath to collapse, destroying the mecha.
After they climb out of the remains of their mecha, Team Rocket recites their motto. Ash's Starly uses Wing Attack, but Jessie calls out Dustox, who blows Starly away with Gust. James tells Cacnea to fire Pin Missiles at Pikachu, but he dodges using Quick Attack. Brock sends out Bonsly. Jessie commands a Gust from Dustox. The first pushes Bonsly back, but the second time the balls on Bonsly's head begin to glow, and Bonsly uses Gust, blocking the attack. Brock realizes that Bonsly has just learned Mimic. Dustox follows up with Psybeam, but Brock tells Bonsly to dodge it and use Mimic. The resulting Psybeam knocks out Dustox. The group charge forward, when Starly flies ahead. As it swoops upwards, Starly starts to glow and it evolves into Staravia. Staravia then uses Aerial Ace to make Team Rocket blast off. Staravia lands, and Dawn checks him on her Pokédex. Rosebay thanks Staravia for its assistance as the other bird Pokémon fly off, with Hoothoot waving goodbye to Staravia. The group leaves Rosebay and continues on their journey, with Staravia flying overhead.