On the night of a full moon, Ash and his friends gaze at the sky as their Pokémon play together. The group spots a shooting star, and they close their eyes to make a wish each. When they open their eyes again, Ash notices the shooting star is behaving strangely. It then soars towards them, revealing itself to actually be a UFO, and shoots out an object which lands on Phanpy's back. Soon, the flying saucer crashes on a nearby mountain, which also catches the attention of the Pokémon Mystery Club.
Ash looks up the mysterious pink Pokémon on his Pokédex, and it turns out to be a Cleffa. Phanpy recovers from its shock and befriends Cleffa. Soon, Cleffa points towards the place where the flying saucer landed. Brock and the others notice Cleffa's concerns, and they decide to help Cleffa return to its friends. Team Rocket is also watching and decides to capture Cleffa. Just then, two people run up to Cleffa and start studying it, identifying themselves as Ken and Mary of the Pokémon Mystery Club, or PMC for short. They ask to take Cleffa, but Ash thinks they may be members of Team Rocket. Ken and Mary are instantly annoyed and call Team Rocket an awful organization. The Rocket trio reveals themselves in anger and recites their motto. The PMC is infuriated by their presence and reveals their machine. The machine shoots out a net, though Phanpy runs off with Cleffa on its back in time. Pikachu uses Thunderbolt on the PMC, creating smoke, and the group follows after Phanpy. While Ash and his friends head toward the mountain, Team Rocket cannot find Phanpy and Cleffa, so they use a divining stick to show which way they went. As they begin to head that way, PMC appears and shows off another machine that resembles a satellite; which soon reveals Cleffa's location. Then, they bring out another machine, which resembles a snowplow. It quickly catches up to Phanpy and Cleffa while they are at a cliff. Phanpy looks around for an escape plan. It resorts to knocking over a tree to use as a makeshift bridge and walks across it.
PMC tries to use harpoons to get to the other side of the cliff, but Team Rocket soars into view aboard their Meowth balloon and blasts away the harpoons. PMC inserts a plunger into the blaster and fires it at Team Rocket, effectively stopping the trio from flying off. Soon, Ash and his friends show up and sneak away while the two teams are fighting. Meanwhile, Phanpy and Cleffa arrive at a hill, as do the group. They see a spaceship at the bottom and realize it is the same Clefairy spaceship they saw before. Ash and his friends also spot Phanpy and Cleffa. Just as Cleffa and the Clefairy are reuniting, PMC shows up, followed by Team Rocket in their balloon. The Meowth balloon transforms into a robot and tries to grab Cleffa. Phanpy stands in the way but is merely thrown aside. Pikachu uses Thunderbolt, but it proves useless against the machine's electricity-proof defense. The Clefairy head into action, just as PMC unleashes yet another machine, a truck with grappling arms. The Meowth robot wrestles violently with the truck, and Team Rocket eventually decides to activate a cannon. However, the Clefairy are taking apart the machine and using the parts to repair their spaceship. Upon seeing this, PMC is confident of their success, but then realize the Clefairy are doing the same to them.
Soon, the spaceship is finished and Phanpy rushes Cleffa to the ship as it starts to take off, but it begins to fall apart. PMC and Team Rocket decide to work together and head towards the spaceship. Pikachu uses Thunderbolt and Phanpy strikes with a Rollout, blasting off Team Rocket and PMC. Pikachu's electricity also energizes the Clefairy ship, which begins to take off. Ash urges Cleffa to jump aboard, but it is reluctant to leave its friend Phanpy behind. The lead Clefairy realizes that Cleffa is left behind. Cleffa suddenly evolves into a Clefairy, and with its new wings, it floats into the spacecraft to reunite with its family. Clefairy offers Phanpy a final wave before the pair make a teary goodbye. Phanpy is saddened about the loss of its friend, but Ash cheers it up.
Another day and the PMC continue to investigate the world's mysteries. In their latest venture, they investigate some crop circles, which they learn have been created by a Snorlax. As the pair gazes at their discovery, Snorlax rolls onto them and pins them to the ground.