Ash and his friends are on their way to the Battle Frontier, and Misty joins them for a while as she heads back to Cerulean City. But Daisy calls to ask if she can start giving away Gym Badges—Misty just can't get a break! Brock has left his Ludicolo at home, May is delighted with her new Squirtle, and Max is eager to see Pokémon that live on nearby Mt. Moon, like Cleffa. Sure enough, a Cleffa appears.
So does Team Rocket and their Poké-Vac 5000, which manages to vacuum up all of the kids' Pokémon except for Pikachu. Except Team Rocket accidentally ejects the Pokémon right back out, the Poké-Vac breaks, and in the confusion as Team Rocket blasts off, Cleffa, Misty, Max, Pikachu, and Azurill all fall in a river!
Misty and Max get back onto dry land and start to look for their friends. Easier said than done, as they run from Beedrill and take cover from a rainstorm. Meanwhile, a Clefairy and Clefable team up with Ash and May to find Cleffa. Just as they find Misty, Team Rocket shows up to spoil the reunion.
Clefairy, Clefable, and Cleffa call for backup, and Team Rocket is on the receiving end of a super-powerful Metronome—Solarbeam combo, with Munchlax on the assist. That's it for Team Rocket until next time! That night, Ash and his friends watch a Pokémon moondance, and in the morning he and Misty go their separate ways once more.
On the way to the first Battle Frontier facility, the Battle Factory, Ash and his friends stop to have a picnic at the foot of Mt. Moon. Ash notices that Ludicolo is missing, and Brock reveals that he left it at home since his brothers and sisters got along with it. Suddenly, Misty gets a call on her Pokégear from her sister Daisy, who reports that the Cerulean Gym is packed with challengers eager to earn their Badges. Daisy wonders if they can just hand out the Cascade Badges in the meantime, though Misty nixes that idea and orders her sisters to be patient before she get home. With that, the group packs up and prepares to head toward Cerulean City. Before departing, they encounter a wild Cleffa.
Team Rocket suddenly appears and traps the group's Pokémon with a vacuum machine attached to the basket of their Meowth balloon. They eventually succeed, but do not get Pikachu. Jessie sends out her Seviper, who manages to land a Poison Tail on Pikachu before he can use Thunderbolt. Meowth sets the vacuum to full power, but due to Jessie's impatient tampering, the machine reverses the suction and returns all the captured Pokémon back to the twerps. Jessie's continued interference causes the machine to malfunction and explode, blasting Misty, Max, Pikachu, Azurill and Cleffa off a cliff and into a river. May tries to grab Max's hand, but fails.
After climbing out of the river, Misty and Max find that Pikachu is weak from the poison he received from Seviper's Poison Tail. Max worryingly affirms that there isn't a Pokémon Center nearby, though Misty has her Azurill use Refresh, which heals Pikachu. Meanwhile, Ash, May, and Brock are searching for the others with the help of Mudkip's radar, but the search fails. Misty's group also sets out to find Ash's group, and suddenly Cleffa runs off to a Pecha Berry tree. Misty gives one to Pikachu before they all sit down on a large cloth to feast on the Berries. Suddenly, three Beedrill suddenly appear out of the bushes, scaring Misty. She runs off with Max, the cloth full of Berries, and the party's Pokémon in tow. They accidentally run off a cliff and fall into in a forested area. Luckily, they are saved from serious injury when they land on a large patch of thick, soft moss. A storm begins to form, frightening Cleffa, so they wait it out in a nearby cave. Meanwhile, Ash's group is taking shelter under a tree, with Cleffa's friends Clefairy and Clefable standing nearby. After finishing off the Pecha Berries, the Pokémon sleep as Misty and Max have a conversation about older sisters. Misty proposes that they both keep helping their sisters, even when they don't think they need it, and Max heartily agrees. They then see that the storm has cleared and resume their search for Ash and the others. May, Ash and Brock do the same, soon finding fresh footprints from Misty's group and follow them.
As Misty and Max continue their search, Team Rocket attacks again with their vacuum machine. Max is about to be sucked up, but suddenly May appears and grabs his hand in time to rescue him. Ash, Brock, Clefairy and Clefable also run onto the scene and are relieved to see everyone is safe. May and Max call Team Rocket out, so the trio respond with their motto and switch their vacuum machine back on. Azurill quickly uses Bubble, which is sucked into the machine instead and causes it to explode, sending the trio plummeting to the ground. Team Rocket then attack with Seviper and James's Cacnea, but Cleffa, Clefairy, and Clefable call their friends, who appear and begin using Metronome. May's Munchlax escapes from its Poké Ball and begins to wave its arms with the Clefairy. The Cleffa use Splash, causing Team Rocket's Pokémon to bounce up and down. The Clefable use Teeter Dance, causing all of Team Rocket dance as well. Team Rocket aren't by this until Meowth realizes that it was only a distraction so Munchlax and the Clefairy could power up Solar Beam. Jessie and James order Seviper and Cacnea to attack with Poison Tail and Needle Arm, but Pikachu stops them with Thunderbolt. Having been given the time to charge, Munchlax and the Clefairy fire their Solar Beams, sending Team Rocket blasting off.
Afterwards Cleffa, Clefairy, and Clefable march off to Mt. Moon. Misty mentions that since tonight will have a full moon, they are probably going to perform a moon dance. Brock explains to May and Max that the Cleffa evolution family dance around a giant Moon Stone on Mt. Moon. When Max asks if they can go watch, Brock says they likely can, as the Fairy Pokémon now trust them. Ash and friends follow them and watch the Pokémon perform their ritual dance around the Moon Stone, instantly putting a smile on everyone's faces. The following morning, Daisy calls Misty once again, demanding to know where she is. Misty tells her that she will be home shortly, ending the call. Misty has to take the other fork in the road, so she and Azurill leave Ash's group to return to Cerulean City not before wishing Ash and May all the best with the Battle Frontier and Pokémon Contests respectively. She reconfirms with Max that both will continue to help their older sisters.