Still in Fennel Valley awaiting the return of Brandon, Ash trains at the Pokémon Center battlefields with his Pokémon. He commands an attack from each of them and all attacks hit the target, a bowling pin for each Pokémon. Meanwhile, inside the Pokémon Center, Brock rushes down the hall to Nurse Joy where they’re going to make breakfast together. He hears the cry of Chansey and runs into a nearby room to find Nurse Joy on the floor, obviously very sick.
Later, Nurse Joy lays in bed as the gang watches over her. Professor Oak mentions that she has the flu. She sits up and tries to go back to work but she begins coughing and Professor Oak pushes her back under the covers, saying that they’ll take care of the Center for her. Outside, Team Rocket slowly stumbles along the road, Jessie saying that Harley sent them so far out that they couldn’t even get a return flight back. They come to a fork in the road and Jessie picks up a stick, tossing it into the air and yelling for fate to choose a side. The stick smacks a Diglett on the head, bounces off and smashes into a Gloom who fires a Stun Spore as a reaction. The spore flies into the air and stuns an Electrode sitting in a tree. The Electrode falls out of the tree, rolls down a hill to a road and bounces onto a bus where it promptly explodes.
At the Center, Max alerts Professor Oak and May to the disaster while Ash and Brock man the Center’s lobby. Ash gets a call about it and they all head out to the crash scene. There, a man stands on the road with several Pokémon, Wooper, Swinub, Seedot, Larvitar, Whismur, and Makuhita while a Bagon stands on the railing looking over the canyon. The team of healers arrives and loads the Pokémon into the emergency vehicle while Scott assesses the damage done to the bus. The man, named Matt, tells them that he was Poké-sitting the Pokémon.
May spots the Bagon on the railing and looks it up in her Pokédex. Meanwhile, Meowth spots that all of the Pokémon could evolve into very strong Pokémon under their care and Team Rocket makes the choice to steal them all. Bagon jumps off the railing and runs away, so Ash and Matt chase after it. In a clearing, Bagon runs up onto a rock protruding from the ground and leaps off of it, smashing into the ground. Ash runs up to Bagon and touches it, trying to help, but Bagon uses Headbutt on it. Matt runs up and says that Bagon is very shy and that it was trying to fly. He continues that if Bagon could only evolve into a Shelgon and then a Salamence, it would be able to fly.
Back at the Pokémon Center, Max takes care of the Whismur, offering it some Pokémon food. Whismur rejects the food and begins to cry. Max begins petting the Whismur on the side and it stops crying, allowing Max to give it the food. Over at the other side of the Pokémon Center, May plays ball with Seedot and Swinub. She spots Larvitar watching them from behind a couch and goes over to greet it. Upon touching it, Larvitar immediately uses Sandstorm. Meanwhile, in another room of the Center, Brock uses Marshtomp’s Water Gun to heal Wooper’s injury. Professor Oak compliments Brock on his abilities to heal and says that it’s a great skill to possess. Outside, Scott works on the damage to the bus while the judge from the Battle Pyramid walks up. Scott asks if there’s been any message from Brandon about when he’s coming back and the judge tells him that there hasn’t been.
Back up in the mountains, Ash and Matt continue their search for Bagon and come to a cliff. Matt says that it was his idea to bring the Pokémon up to Fennel Valley where it is very pretty indeed. They spot Bagon on a cliff over a raging river and rush down to it as it jumps off, trying to fly again. And once again, it fails, landing in the river which sweeps it away. Ash and Matt chase after it on the shore and Bagon manages to cling to a rock. Several Carvanha attack it and Ash has Pikachu blast them away with Thunderbolt. He then throws a log out to Bagon so that it can use it to walk to the opposite shore. Before it can reach the shore however, several Carvanha begin gnawing at the log, eliminating Bagon’s escape. Ash sends out Sceptile and has it help Bagon get to shore. It does this by jumping onto the end of the log (which Bagon is standing on) and sending it flying through the air back to Matt. As it flies, Bagon tries to fly of its own accord but fails again and lands in Matt’s arms. Matt quickly realizes that it has a fever and they take it back to the Pokémon Center.
Professor Oak and May are taking care of Nurse Joy while Chansey watches as Larvitar walks into the room. Professor Oak walks over to it and touches it, setting off another Sandstorm. As Bagon is brought in, everyone rushes to its side and Brock and Professor Oak take it into the Emergency Room. That night, Professor Oak and Brock continue to work on Bagon as Team Rocket prepares their plan. May brings out food for all of the Pokémon and they eat happily. As they do, Team Rocket comes into the Center in disguise, saying that they are Assistant Poké-sitters and they’ll be taking over for the Pokémon. They quickly load all of the Pokémon in sight into a cart and take off, leaving behind their signature Smokescreen as they do. Meanwhile, Bagon seems to be doing better but suddenly its temperature skyrockets and Nurse Joy arrives on the scene, feeling just fine.
Outside, Team Rocket makes their getaway as they’re chased by everyone not caring for Bagon. They say their motto and Ash begins to tell Pikachu to attack. Jessie pushes a button, opening the cart and allowing the Pokémon to stick their heads out. She remarks that Ash’ll be attacking the Pokémon too if he allows Pikachu to use an electric attack. Inside, Nurse Joy gives Bagon some medicine and its temperature stabilizes. Back outside, May tells Larvitar to use Sandstorm, which it does, and Team Rocket comes crashing to the ground. The Pokémon free themselves from the cart and rush back to Matt while Jessie and James send out Seviper and Cacnea. Cacnea promptly hugs James before launching an offensive with Seviper. Pikachu makes quick work of the evil trio with Volt Tackle as Brock runs out with the good news that Bagon is okay.
The next morning, everyone gathers outside, the Pokémon healed and the bus fixed by Scott’s “all-nighter.” The Pokémon say their goodbyes to their respective new friends and load up into the bus, leaving with Matt and waving from the back as they drive out of sight. Just then, the judge of the Battle Pyramid runs up and tells them that Brandon has found the Pokémon he’s looking for and shall be back soon. The sun shines brightly on Fennel Valley as Ash exclaims that he’s ready.
