The episode begins with Ash, Brock, Misty and Pikachu walking along a path towards Cerulean City. They suddenly hear a scream and find a flock of Zubat attacking a man. Ash has Pikachu use ThunderShock to send the Zubat flying back into the cave. A grateful Seymour springs to his feet and hugs Ash so tightly that Pikachu uses thunder shock to break free. The man then begins to thank Ash through poetry and then reveals his name to be Seymour, Seymour the Scientist. They then go inside the cave where they see the inside of the cave light up, with many Paras planting their mushrooms and a Sandshrew, exhausted as the lights is drying it out.
Misty asks Seymour why someone would attack the cave and Seymour then begins to explain his theory about the Moon Stone, stating that the Moon Stone is from outer space and helps to increase the power of the Pokémon, again using poetry to express himself. Misty states that is an original theory and after Ash nervously agrees with Seymour's theory, a Clefairy hops past holding a small rock. Ash attempts to capture Clefairy but is stopped by Seymour, explaining that Clefairy should be allowed to live in the cave.
Clefairy, who has gone down a side tunnel, cries out for help and is shown in a dead end, with the shadow of Team Rocket's Meowth shown over it. Ash then realizes that Team Rocket is behind the lights in the cave and, after doing their introduction, they admit to their plans to steal the Moon Stone to power up their Pokémon. Jessie and James state that Ash is only jealous because they won't allow him to join them, with Ash declaring that he would never join Team Rocket. A battle then ensues, with Team Rocket sending out Ekans and Koffing, with Ash sending out Butterfree and Brock sending out his new Zubat, which he announces he caught when entering the cave. Koffing uses Smog, which is blown away by Butterfree and Zubat's Whirlwind attacks. Ekans uses its Bite attack on Butterfree and Koffing its Tackle on Zubat. Meowth is shown sneaking away as Zubat uses Supersonic. A confused Ekans and Koffing begin to attack themselves, much to the shock of Jessie and James. Ash capitalizes on Team Rocket's lack of focus by commanding Butterfree to use Whirlwind, which results in powerful winds that cause Ekans and Koffing to slam into their owners. Jessie and James are lifted off the air and are promptly blown out of the cave.
Ash and Brock, however, notice that Meowth was not blown away with Team Rocket. Clefairy is then shown leaving the cave, with Misty and Seymour following close behind. Meowth then reappears on a narrow bridge, with Clefairy jumping off and hitting Misty, causing her and Seymour to fall into some water. Meowth follows but is quickly defeated by Misty's Staryu, after Swift and Water Gun. Misty then recalls Staryu and then episode cuts to the evening, with Brock feeding Zubat and then Butterfree with Pokémon food. Seymour tries the Pokémon food, stating its 'not bad'. Ash also tries some, although he does not like the taste.
Pikachu is then shown talking to Clefairy and, when Ash notices, the two leave with Ash, Misty, Brock and Seymour following. They find and enter another cave, where they find the core of the Moon Stone, sparkling in the moon light. Clefairy puts a small piece of the Moon Stone at the base of the core, with the small pieces lighting up. The Clefairy then begin to jump and twirl, in unison, around the Moon Stone, except for the Clefairy that Ash, Misty, Brock, Seymour and Pikachu followed. Pikachu then attempts to tell Ash the reason the Clefairy like the Moon Stone. They eventually realizes that Pikachu is telling them that Clefairy pray to the Moon Stone, with Seymour then stating that his theory is surely true.
Team Rocket then re-appears and challenge the gang once again, for the Moon Stone. A nervous Seymour stands up to Team Rocket and runs towards them, but he is tripped up by Meowth, losing his glasses in the process. Jessie and James once again bring out Koffing and Ekans, with Pikachu and Onix being used by Ash and Brock. Jessie tells Ekans to dive underground whilst Koffing uses Smokescreen to cause a distraction. Ash brings out Pidgeotto to blow the Smokescreen away and the gang realize that Team Rocket have dug a large hole and escaped with the Moon Stone.
Brock has Onix follow them down the hole and the three run out of the cave. A Clefairy hands Seymour his glasses and Seymour tells them that they should be trying to get the Moon Stone back. Jessie, James, Meowth, Ekans, and Koffing are then shown sliding down the mountain with the Moon Stone, laughing at their successful steal. Their joy is ended by Onix, who knocks the villains off their platform after emerging from the ground. Seymour and the Clefairy then appear out of the whole and all the Clefairy then begin to use Metronome, waving their fingers in the air. Ash, Misty, Brock, Seymour, Jessie, James and Meowth look on and watch, waiting to see what happens, with Misty and Seymour talking in line with the Clefairy's Metronome. The Metronome causes an explosion, with Team Rocket blasting off into the distance.
The Clefairy's Metronome is then shown to have caused a hole to appear in the ground and the core of the Moon Stone to have seemingly been destroyed. Pieces of the Moon Stone then begin to fall out of the sky and some land on some of the Clefairy, causing them to evolve into Clefable. The episode then cuts to Clefairy and Clefable dancing around the core of the Moon Stone back inside the cave. Seymour then announces his intentions to live with the Clefairy and Clefable as it was his dream to find the Moon Stone and that, one day, he will travel into space with them.
Ash, Misty, Brock and Pikachu then leave the cave and Seymour behind, with Seymour, the Clefairy and Clefable waving them off. The three continue to walk towards Cerulean City where they see a sign pointing them in the right direction. Misty seems to be quite upset about this. Brock, however, notices that someone has written on the sign. Ash takes a closer look and sees that it was Gary, who had written that Ash 'is a loser'. An angry Ash then runs off to try and catch up with Gary, with Misty, Brock and Pikachu running after him.
