Ash and friends are still exploring Izabe Island on the way to Sootopolis City. They have come across a desert landscape with tons of holes. Max informs everyone that he can’t find their location in the PokéNav.

Looking through the guidebook, Brock can’t find a map of Izabe Island. The four friends notice that each of the holes is exactly the same size. Ash picks up a rock and tosses it into a hole. Just as it reaches the bottom, a Trapinch pops it head above the surface of the ground and gobbles up the rock. Ash pulls out his Pokédex and looks it up.

A voice cries out and everyone turns to see a woman pulling up in a vehicle. She gets out and introduces herself as Elisa. Brock quickly falls in love with her but is distracted by the ground breaking out from under Ash. Ash begins to slide down; Elisa throws her rope down to him and she pulls him up.

Elisa tells them that the holes were all dug by Trapinch and they are the entrances to the Trapinch Underground Labyrinth. She is working on a map of the Labyrinth but as it is ever expanding, cannot finish it completely. Everyone gets into Elisa’s car and she takes them on a tour of the area. Tons of wild Pokémon live there including Girafarig, Nidoran, Rhyhorn and Rhydon.

Another voice calls out and everyone spots a man running from an enraged Donphan. Elisa quickly gets out of the jeep and releases a Meganium having it use Sweet Scent to distract the Donphan. Having calmed down the Donphan, Elisa recalls Meganium. The man introduces himself as Hal: an Izabe Academy Pokémon Researcher. He explains that he is tracking a Trapinch to help with the mapping of the Labyrinth.

Underground, Team Rocket has concocted another machine. This time, they have a Diglett with a periscope. They spy on Ash and the others while formulating a plan.

Back above the ground, Hal explains that ever since he was a kid, he has been searching for an underground lake. When he was young, he ventured near a Trapinch hole and the ground collapsed under him. He slid to the bottom of the pit and the ground swallowed him up like quicksand. When he awoke, he was in a beautiful cavern. In the cavern was a lake and tons of grass. At the other side of the lake, a huge group of Trapinch was gathered. Suddenly, they all began to glow and evolved into Vibrava. The Vibrava took to the skies and left the cavern through an opening above. Hal watched them until they were out of sight and then realized that they had carried him out of the cave.

Ash pulls out his Pokédex and looks up Vibrava. While Hal was telling the story, the Trapinch he was tracking left but no one dwells on that fact as Team Rocket emerges from the ground in their mechanical Diglett. They start off with their motto again and then use a giant claw (again!) to steal Pikachu. Brock releases Ludicolo who immediately begins dancing with Max. Brock has Ludicolo use Water Gun which knocks the Diglett into a Trapinch hole. Lots of Trapinch emerge from the ground and begin eating the Diglett leaving Team Rocket and Pikachu to be pulled into the Labyrinth.

Ash wastes absolutely no time and dives in after his Pokémon. Elisa also follows. The path from the Trapinch hole branches off a little ways in and, while Team Rocket goes one way, Ash and Elisa go another. Trapinch appears behind Ash and Elisa as they land in an underground passage. Up above the ground, the others watch as Hal gets some rope and a locater screen. He explains to them that it shows where Trapinch is and continues walking towards the hole while talking. He slips and falls in and then begins searching for Trapinch.

Ash calls out desperately for Pikachu as Elisa notices Trapinch. She points it out to him and suggests that they follow it.

Once again, Meowth imagines Giovanni’s face as he gets his new Trapinch. Hal comes out of a tunnel behind them but doesn’t notice them and keeps going. Team Rocket notices him and they begin to follow him. Outside Max, May and Brock decided to follow and jump in the hole. Miraculously, they end up together and right in front of Ash, Elisa and Trapinch. Without any warning, Trapinch goes over to a wall and digs through it just as water begins to rush through the tunnel. They all try running but the water’s force pushes them through the tunnel and they end up in the lake.

At the edge of the lake, Pikachu waits for them. Ash quickly joins it, followed by his friends. The Trapinch also ended up at the lake, as did Hal. Team Rocket is also there and they hide waiting for the right moment to steal the Pokémon. Elisa apologizes for not believing Hal when he said there was a lake. She tells him that deep down she did believe him and blushes. The Trapinch all gather at the other shore and begin to glow. The Trapinch that Hal was tracking’s transmitter falls off as it begins to grow.

When the glow faded, Vibrava stood where the Trapinch were seconds before. Team Rocket attacks before anyone can do anything and the Vibrava are captured in a net. They lift off in their balloon, thinking their plan actually worked.

Brock releases Ludicolo who begins to dance with Max again before using Bullet Seed. Elisa’s Meganium helps release the Vibrava which angers Jessie and James. They release Dustox and Cacnea who gives a pokey hug to James. Dustox uses Poison Sting and Cacnea uses Pin Missile. The Vibrava block their attacks with Supersonic. Pikachu uses Thunderbolt and Team Rocket is blasting off again shouting, “How predicable!”

Ash gets an idea and gets the Vibrava to carry them out of the cave, May complimenting him on his idea. That night, everyone says goodbye to Elisa and Hal as the sun sets. Hal voices that he wants to keep the underground lake a secret and let the Trapinch live peacefully, also mentioning that he only wanted to find it for Elisa. They blush as Ash and friends walk away.