The Nurse Joy at Lake Lucid's Pokémon Center is famous among Water-type Pokémon Trainers, so Misty is thrilled when our heroes' travels take them to the lake. Lake Lucid's Nurse Joy is the third generation of Nurse Joys who have turned Lake Lucid from a toxic pool to a crystal-clear lake where Water-type Pokémon come to rest and recuperate, and she's one of Misty's long-time heroes.
Everything goes swimmingly until Misty asks Nurse Joy to examine her Water-type Pokémon. This Nurse Joy actually hates Water-type Pokémon, and she's hated them ever since some Remoraid frightened her when she was a child! Even though Nurse Joy says she still understands Water-type Pokémon and doesn't let personal feelings impair her ability to do her job, Misty refuses to believe a word of it. She's angry and distraught that her idol doesn't even want to touch Water-type Pokémon without putting on a special protective suit.
Misty's tour of the Pokémon Center is interrupted by Team Rocket, who burst in with a beat-up Tentacruel submarine and try to steal the Center's Pokémon. They're soon defeated, but Nurse Joy's protective suit is lost and a Gyarados becomes agitated when its tank is destroyed. As the only one with the training and experience to handle the situation, Nurse Joy steps up and calms Gyarados down, suit or no suit—she may hate Water-type Pokémon, but her duty takes precedence over fear. Even though Nurse Joy isn't magically cured of her hatred for Water Pokémon, Misty realizes she may have judged too harshly and leaves with a newfound respect for Nurse Joy's dedication.
The group arrives on the shores of Lake Lucid. Misty is particularly keen, as the local Pokémon Center is famous for its specialty of caring for Water-type Pokémon. As they look, Pikachu notices bubbles in the water, and suddenly a person in a full scuba suit holding a Goldeen emerges. The person orders her two Chansey to replace Goldeen's bandages and promptly places it in a water stretcher; what resembles a fish tank on wheels. A Nurse Joy emerges from her scuba suit, but she is quickly overwhelmed by Brock's affection. Misty pushes him away, but she is too star-struck by Nurse Joy to say anything herself. Joy turns her attention to Pikachu, and invites everyone into her Center while Pikachu gets treated for his exhaustion.
Nurse Joy details the polluted history of Lake Lucid and explains that her grandmother and mother's efforts have led to the pristine environment seen today. Brock attempts to get Nurse Joy to sign two books published by her family, but Nurse Joy admits that she isn't the author and so it wouldn't be authentic if she signed them. The group admires the various Water-types, and watches as they battle each other, which Nurse Joy explains is how the Pokémon keep fit. Brock credits their health to the world-class care given to them by Nurse Joy. He reaches into his backpack again, looking for Nurse Joy’s book. She admits that she hasn't written anything yet, but is planning to publish "An Autumn harvest of Pokémon".
Meanwhile, James looks through the periscope of the Tentacruel submarine and spots Nurse Joy talking to Ash and his friends. Team Rocket inch closer to their targets when they are dragged down by an actual Tentacruel. Meowth translates Tentacruel’s speech and reveals that it is keen for a battle. Tentacruel sends out a powerful Supersonic which instantly takes effect on the Rocket trio. They surface from the lake just as Joy takes the group into the Center.
Nurse Joy gives Pikachu a recharge, and he feels instantly energized. Misty asks Nurse Joy to check on her Pokémon as well, and she kindly agrees to do so. Misty presents her Poké Balls to Nurse Joy and admits that she has a team of Water Pokémon, but Nurse Joy instantly backs away seemingly in fear. The group is taken aback when Nurse Joy declares that she actually hates Water Pokémon. She admits that she would be happy to treat them, only if she is wearing her protective dive suit. Nurse Joy dons her dive gear and offers to take Misty's Pokémon in for treatment, however, Misty's feelings are hurt and she refuses Joy's services. Joy assures Misty that her preference doesn’t affect her ability to perform her job. Misty decides that she’ll carry her Poké Balls into the treatment area, and Joy admits that she is grateful as her dive suit's claw hands don’t really allow for much movement. The group tours the treatment area, where Misty is then startled by a large Gyarados after it roars. Nurse Joy admits that everyone has something they fear. She explains that she has designed various treatments and diets for Water-types and looks forward to publishing her findings. Misty questions Nurse Joy's level of understanding, but Joy affirms that she doesn't need to be emotionally involved to properly treat her patients. Brock thinks Misty is being too harsh, but Misty expresses her deep disappointment for her idol's attitude towards Water Pokémon. Nurse Joy sincerely apologizes to Misty and admits that an incident led her to dislike Water-types. She explains that she was in a boat with her mother to investigate an increase in Lake Lucid’s Remoraid numbers. Suddenly, a Remoraid appeared and squirted her in the face, causing her to fall into the water. Joy soon found herself surrounded by a school of Remoraid, and while she was eventually returned to the boat, the incident left her fearful of all Water Pokémon. Misty remains disappointed by her idol, but Joy declares that she is happy in her nursing role.
Suddenly Team Rocket's Tentacruel sub appears in front of Joy and the group. Nurse Joy is quick to spot the fake which leads the Rocket trio to reveal themselves. They dive into the pool and perform their motto while performing a water aerobics routine. The trio jumps back into their mecha and sends out a tentacle to grab Pikachu, however, he dodges. They eventually ensnare Pikachu with several tentacles. Ash orders Pikachu to use Thunderbolt. James declares that the attack will have no effect on their rubber-constructed sub. Jessie is skeptical and reminds James that they have just been in the water, which is known to conduct electricity. The mecha eventually explodes and some of the debris shatters Gyarados's tank. Another piece hits a control panel, and Team Rocket are sucked out of the Center as a result.
Gyarados's glass tank eventually cracks completely, and the surge of water washes Joy's protective suit outside as well. Soon Gyarados falls out of its tank, and it breaks free of its strengthening neck brace. Ash rushes to assist, but Brock is concerned that Gyarados might lash out. Gyarados starts writhing in pain for a while. Joy takes a stand and decides to help out Gyarados for now, even without her suit. She approaches it, and despite her nerves, she persists. Nurse Joy calms Gyarados down by gently patting its crest and the Chansey get another cast for Gyarados and place it on. Soon afterward, Joy collapses from holding in all that shock. Afterwards, Joy still says she doesn't like Water Pokémon, but as a Pokémon nurse, she has to try her best. Misty gives her some encouragement and the gang heads off to their destination.