Ash is finally training for the Pokémon League, and is battling Brock. Ash's Pikachu is battling Brock's Vulpix. Pikachu is about to use Thunderbolt, and Vulpix is about to use Flamethrower, when Jigglypuff appears in-between them. At Ash and Brock's command, Pikachu and Vulpix fire their attacks in a different direction, destroying a rock wall. As Ash and his friends walk closer, they see that they have uncovered the entrance to a temple, as well as a gigantic bell. They find an ancient artifact in the rubble, and an archaeologist named Eve takes it.
Eve and the other archaeologists are digging up artifacts related to the ancient city of Pokémopolis, and a professor finds a spoon similar to the first artifact. Pokémopolis was destroyed in a storm a long time ago, and an ancient tablet reads that two great powers of destruction will fight and destroy the world, and no human knows the secret to stop them.
That night, Team Rocket attempts to steal the rare and valuable artifacts from the temple. Jessie has her Arbok enter the temple and bring back the most valuable thing it can find. It brings back a dark object that appears to be three dark orbs together. It absorbs Arbok, and chases after Team Rocket. It makes footprints in the ground as it chases them, as though it is invisible. It absorbs them as well, offscreen.
Next day, the professor finds the dark device, and is absorbed by it. It then absorbs all the archaeologists except Eve, and turns into a giant Gengar with strange markings on it. Gengar heads to the nearest town to destroy it. As the nearest town is Pallet Town, Ash tries to stop it. Ash, Misty, and Brock chase after it while Eve heads back to the van, where the artifacts are floating around. He sends Pidgeotto after it, but the Gust Attack doesn't do much, and Pidgeotto is absorbed by Gengar. Brock sends Onix after it and has Onix use Bind, wrapping around Gengar's leg, but Gengar absorbs it too.
Gengar chases Ash, Misty, and Brock back to the van, where Eve is possessed by the two strange artifacts (the one that looks like a spoon and the other one with the same design), and the spoon sticks in the other one like a key, and the spell on Eve and the other artifacts is broken. The two artifacts then transform into a giant Alakazam, also with strange markings on it. Gengar and Alakazam battle. Alakazam shoots energy waves that, when they hit the ground or a wall, transform into strangely-shaped stones. What those are is unknown. Gengar and Alakazam enter a beam struggle with Night Shade and Psybeam respectively, and where the beams collide, they shoot into the sky, threatening to destroy the entire planet.
Ash has his Pikachu use Thunderbolt on them when they step into the water, but although they are affected, no significant damage is caused to them. Then, Jigglypuff appears and sings its song. Everyone inside the giant Gengar falls asleep, but Gengar and Alakazam do not, as Jigglypuff is too small to put them to sleep. Gengar knocks Alakazam backward, and it crashes into Jigglypuff, sending it flying into the distance, Team Rocket style.
However, Jigglypuff's song makes the giant bell glow, and it summons forth a giant Jigglypuff. The giant Jigglypuff's song is loud and powerful enough to put the giant Gengar and Alakazam to sleep, as well as Ash, Misty, Brock, Eve, Pikachu, and Togepi. Just like the regular Jigglypuff, the giant Jigglypuff gets angry when it sees that Gengar and Alakazam fell asleep, and pulls off the head of the bell, revealing it to be a paintbrush, and scribbles on Gengar and Alakazam's faces.
When Ash and the others wake up, the dark clouds have vanished, as have the three giant Pokémon. The artifacts and all the giant Gengar's victims have all reappeared. Ash walks up to Team Rocket, and they decide not to battle Ash this time, and run off.
So the mystery of Pokémopolis has been solved, but the biggest mystery has yet to be solved - will Ash ever get to training for the Pokémon League?