Making their way through a dense forest, Ash, Misty, and Brock find themselves caught in an unexpected heavy downpour. Looking for shelter, Pikachu spots a mysterious-looking castle not too far away.
Approaching the front steps, the door suddenly opens. Inside, our heroes hear moans and cries of pain echoing throughout the building. As they close in on the sound, Brock figures that it must be a torture chamber of some kind. Barging through the next room, the gang instead finds several Pokémon performing different medical tasks. A young woman, Dr. Anna, spots our heroes and figures that they must be patients. Ash corrects her, while at the same time, Brock approaches the doctor with his usual charming ways, offering to be called by one of his more "affectionate nicknames", such as "Rocko Brocko", "Lover", or "Brockie". Misty suggests "Insane".
One of the assistants enters to inform Dr. Anna that the Zubat Scan is ready. She runs the scan on one of her patients while her Zubat, Mimi, flies overhead. Telling him that he looks perfectly fine, Dr. Anna offers a Machoke massage for the patient. He complies, and leaves the room. Looking on, Brock realizes that the Zubat Scan is similar to an Ultrasound Checkup, using the Zubat's supersonic waves to check a patient's internal health. Dr. Anna adds that she also uses a number of other Pokémon for diagnostics and treatments, such as Machoke's strength for massages, Spinarak's web for bandages, and Mareep's electricity for low-voltage muscle stimulators. Misty asks why she doesn't operate in a normal hospital. She explains that the owner of the castle was one of her patients, and when she moved away, she allowed her to set up her clinic here.
As Dr. Anna goes back to work, Brock lets out his Zubat, suggesting that he can help her with her rounds. They go off, leaving Ash and Misty behind, who decide to look for lunch instead.
Meanwhile, Team Rocket sneaks about someplace else in the castle. Meowth smells something nearby, and the three come across a room filled with a week's supply of food. James bags the food up as Jessie and Meowth eat the rest, but suddenly, Ash, Misty, and the assistant enter the room as well. Spotting the gang, Team Rocket decides to flee. As they run past Brock and Dr. Anna, she asks whether they have an appointment. Team Rocket does a different version of their motto, speaking of "eradicating the evils of Athlete's Feet" and "scratching at the speed of light". Ash catches up and sends Pikachu, but Team Rocket runs down a hall. Dr. Anna gives chase, warning them not to go that way. Brock follows, and they fall down into a strange maze along with Team Rocket and the Zubat.
Recovering from the trap, Jessie, James, and Meowth decide to follow their own path, when one of the doorways seals shut in front of them. Brock wonders how they're going to find their way out. Dr. Anna brings out a laptop, and orders Mimi to use Supersonic. The Supersonic attack brings up a partial map of the maze. Brock orders his Zubat to use Supersonic, and the rest of the map is completed. Now with some knowledge of where to go, the group presses on.
Still inside the castle, Ash, Misty, and the assistant study a map showing the only exit of the maze, a secluded spot in the middle of the forest. At the same time, Dr. Anna comes across a fork in the road, with both routes having traps.
Back to the other group, Ash finds the exit buried under a giant pile of dirt. Everyone begins digging, having Pikachu, Togepi, Geodude, and Pineco help. Still trying to figure out which path to take, Dr. Anna tells the group that the situation could take some time. The impatient Jessie decides to go through the left passage, with Wobbuffet following. A wall comes up through the way Jessie goes, and she falls down. Dr. Anna realizes that one path becomes safe as the other one is taken. Outside, the gang continues to dig.
Dr. Anna stops the group again, seeing another trap in front of the group. Jessie once more braves through, but this time, pushes Wobbuffet in front of her to become the tester. When she realizes that nothing happened, Jessie walks through, when suddenly, the walls collapse on top of her. Dr. Anna now realizes that a floor panel must be activating the traps.
Ash finally sees part of the exit through the dirt, and keeps on digging while Brock and Dr. Anna notice the Zubat have found a way out of the maze. Brock begins going into one of his fantasies, dreaming of working with Anna forever and getting married. Meanwhile, James notices that the Zubat are very talented, when Jessie mentions that that's why they're going to steal them.
Dr. Anna finds the doorway to the exit, while outside, Ash, Misty, and the assistant finally clear the dirt around the doorway as well. They give a mighty push, but the door doesn't budge. Inside, as Anna thanks the Zubat for a job well done, Team Rocket bags the Pokémon and runs away, but runs into the unmovable door. Back outside, the gang still can't get the door open. Pineco approaches it and begins to self-destruct. An explosion follows, and the Zubat fly out of the bag amidst the smoke. Anna and Brock run out, and is reunited with the rest of the group. Misty notices that Team Rocket is nowhere to be found, when suddenly Pikachu is roped and put into a glass jar.
They make their escape, while James sends out Weezing as a Smokescreen cover up. Mimi and Brock's Zubat blow the smoke away, and Jessie sends out Arbok. Brock commands Zubat to use Supersonic, confusing Arbok and making it attack Team Rocket. Suddenly, Brock's Zubat begins glowing white, and evolves into Golbat. Arbok recovers and uses Poison Sting on Golbat. It uses Wing Attack to block the projectiles, retaliating with Supersonic, sending Arbok and Weezing down for the count. James drops Pikachu's jar, and the glass breaks. Pikachu finishes Team Rocket off with Thundershock, and Team Rocket is sent blasting off again.
Back inside the castle, Dr. Anna bandages a wound Brock received on his arm as he tells his new Golbat that, from now on, they're probably going to have to use Supersonic to help out Anna's patients. However, she interrupts Brock's fantasy, telling him that his Golbat's Supersonic attack is too strong, since it overloaded her computer as they were battling Team Rocket. She tells Brock that she's impressed and that he raised his Zubat well, since a Pokémon's powers are usually not developed right after evolving. Devastated, Brock thanks her for the compliment.
With Brock's dream shattered, Ash and Misty drag him away as he and his Golbat make their goodbyes.