As Ash and his friends are riding on Lapras through the waters, a very tan woman resembling Nurse Joy and her Chansey speed past them on a kayak. Ash orders Lapras to follow the kayak and catch up to it. They arrive at a small island, where they find the kayak on the beach and two pairs of footprints in the sand, one of them from a Chansey. After following the footprints to a small bay, they realize there are no more tracks to follow. Misty states her uncertainty that what had passed them on a boat was a Nurse Joy. Tracey recalls the moment, saying that the woman seemed more muscular than an average Joy.
Just then, a giant Magikarp jumps up out of the bay and begins flopping around on the rock at the group's feet. Misty, worried that the Water Pokémon will run out of air, proposes that they help it get back into the water; Ash agrees. Before they can figure out how to help the Pokémon, Nurse Joy and Chansey appear to help Magikarp. Joy gives Magikarp a bottle of Calcium tablets and throws it back into the water. She then tells Ash and his friends that she travels from island to island helping sick and injured Pokémon, because a lot of the Orange Islands are too small for Pokémon Centers. She invites the group to her local clinic for lunch.
Back at her clinic, Joy demonstrates her abilities by treating Lapras. Eager to see her in action, Ash and his friends ask if they can help with her work. As a result, they all set off in kayaks and engage in a variety of situations where Nurse Joy's assistance is needed. A little while later, the group falls behind in their kayaks and loses sight of Nurse Joy. When they finally catch up to her kayak, it is empty, annd both Chansey and Joy are missing. Tracey believes that a Gyarados could have tipped her boat over. Suddenly, they see a pink figure appearing from the water, but it is only Jigglypuff. Before it can begin to sing, they race away in their kayaks.
When they finally stop, they see Joy and Chansey, with its first-aid kit, pop up out of the water. Joy explains that she went underwater to treat a sick Cloyster, and sends Chansey to retrieve their kayak. Ash and Tracey become curious as to how Joy can treat Pokémon underwater, so she offers to show them. The boys get into their swimming attire, jump into the water, and follow Joy to the ocean floor. There, they see a sick Shellder, just as Ash begins to struggle from a lack of oxygen. Just then, a wild Dewgong grabs onto him with its fins and begins playing with Ash. Nurse Joy rescues him and they all head back to shore.
At the clinic, Ash is warming up under a blanket with a hot beverage. The group collectively states that Joy's job is not easy, and that it would be easier to just run a Pokémon Center like all of the other Joys. Just then, she recalls a childhood incident where she found a tiny injured Magikarp on the beach, and decided to take it home and nurse it back to health. When the Pokémon was healthy once again, she released it back into the ocean. A little while after that, while on a boat with her family, she fell into the water; she was then promptly saved by the same Magikarp, who had grown considerably. Joy says that was when she decided to dedicate her life to Pokémon, especially those without Trainers to care for them. Misty asks her whether the Magikarp they saw earlier that day was the same Magikarp she helped. Joy says that it was, and that they have been friends ever since that day.
Outside, the group sees the warning signs of an upcoming storm. When Joy explains that she has one more stop for the day, Tracey expresses his concern and says it is too dangerous for her to go out in the water again. She counters that there is a group of sick baby Seel waiting for her help. Despite Tracey's pleas, Joy leaves on her kayak with Chansey. Worried for her safety, the group follows her without her knowing.
In the middle of the ocean, the choppy waves are making it difficult for everyone to control their boats. Ash shouts for Joy from behind, and she looks back in surprise. Just then, a huge wave sends Ash, Misty, and Tracey flying out of their kayaks. Joy yells at them to send out their Water Pokémon to help keep them afloat, which they do, and they follow her to a nearby island. As they arrive, the storm settles. Tracey apologizes to Joy for intervening, and she accepts the apology. Before continuing on their way to help the Seel, they decide to take a short rest.
Meanwhile, Team Rocket is spying on the group from their Magikarp submarine. Intent on capturing Pikachu and Chansey, Meowth tells James he has a new secret weapon. He then hits a button, which sends a torpedo-like object flying from the submarine, up and out of the water. The object releases a net that entraps everyone on the beach. Appearing from the water in the submarine, Team Rocket recites their motto. Just then, Team Rocket's submarine is attacked by the giant Magikarp befriended by Joy. As Joy calls out to the Pokémon for help, it begins to evolve. Using its newly formed tail, Gyarados whips Team Rocket off into the distance. Gyarados turns around to look at the group, and they begin to worry that its evolution caused a change in its demeanor. It lunges towards the shore, but, instead of attacking, Gyarados gets close to Joy so she can pet it. It then removes the net with its mouth. Misty exclaims that the Pokémon evolved into Gyarados, but kept Magikarp's personality, while Joy thanks her friend for its help. This allows her to reach the island of Seel and treat them.
Ash, Misty, and Tracey admire the relationship between Joy and Gyarados. Joy then remembers Ash telling her of his plans to become a Pokémon Master, and tells him of Navel Island, which is home to an Orange League Gym. As a result, the group heads on their way there atop Lapras.