Upon arriving at Hamlin Island, Ash and his friends learn of a ferry line that runs from Hamlin straight back to Pallet Town. On their way to the ferry, the trio comes to a road bridge, but it is blocked due to extremely dangerous conditions. With no other way to get to the ferry dock on the other side, Tracey suggests they cross it anyway. Just then, a huge Explosion blows apart the middle of the bridge. The three then find a rowboat and make their way across the small stretch of ocean. When they arrive at the town, they find it to be deserted. The three enter the ferry's waiting lounge but come across a locked door that prevents them from getting out to the dock and the ferry itself. As Ash and his friends ponder on how they will get back to Pallet Town, Togepi wanders out of the building and comes across a playful Voltorb, who rolls away. Seeing it as a game, Togepi runs after the Voltorb.
Upon noticing Togepi's disappearance, Ash and his friends search for it and soon find it standing atop the Voltorb. Ash checks his Pokédex for Voltorb's data, and the trio is shocked to learn that Voltorb may explode without warning. Misty attempts to pull Togepi off, but Togepi picks the Voltorb up with it. At that moment, the group is confronted by a horde of Electrode, who are all sparking with electricity. As Ash and his friends try to slowly retreat, a gust of wind knocks over a wooden sign, startling the Electrode and triggering a chain reaction of explosions. Just then, a man appears and throws out several Poké Balls, which release Diglett everywhere. Ash looks up Diglett on his Pokédex and finds out that they dig tunnels under the surface. The mystery Trainer then tells the Diglett to dig the Electrode underground. The Diglett create holes under the Electrode who safely explode underground. The stranger then tells the group to follow him.
At another building, the man tells Ash and his friends that the island used to be filled with people and tourists, but one day, a Voltorb managed to escape from a Pokémon electricity experiment. Soon after escaping, the Voltorb began to multiply, and quickly evolved into Electrode. The Electrode became so numerous that they outnumbered the people on the island. The lack of space caused the Electrode to become irritated, and they started exploding, causing mayhem on the island. People started leaving immediately and the town ended up being deserted, which in turn put the ferry out of commission. Tracey asks why the man is still on the island and Ash suspects he may be a thief. The man laughs it off and introduces himself as Poncho, a Diglett Rancher hired by the town mayor to get rid of the Electrode. He tells the group that he trains his Diglett to dig a large tunnel from under the small island all the way to a prairie behind the city on Hamlin. His plan is to have the Electrode roll from the island to the prairie, making the island safe once again and giving the Electrode freedom.
After Poncho finishes his story, the mayor's office calls with a message to fire Poncho, believing his methods to be too slow, also revealing that the mayor hired someone else to take care of the Electrode. At that moment, a machine emerges from the ocean and drives on land. Team Rocket appears and spouts their motto before revealing the mayor hired them and their "Electrode Eliminator" machine to remove the Electrode quickly. Misty asks why Team Rocket would want to help remove the Electrode; Jessie and James tell them that they are getting paid well and they are planning on keeping the Electrode that they move. They retreat to the machine and race off to find some Electrode. The machine's arms pick up the Electrode, put pressure on them, and force them to explode before putting them in the machine's storage hold, with Ash and his friends being legally unable to stop them.
Electrode from all over the island soon make their way over to Team Rocket's machine. Poncho notes that the Electrode are extremely angry and Tracey points out that the condensed explosions of the huge number of Electrode could destroy the entire island. The friendly Voltorb approaches Team Rocket and they decide to blow it up. Togepi begins waving its arms before they start glowing blue in an attempted Metronome. Togepi begins hopping up and down performing a Splash and Misty thinks that it may be trying an attack. Tracey and Ash brush it off and say that Togepi is too young to know any moves. With the Metronome unsuccessful, Togepi then runs out to assist Voltorb, prompting Pikachu to use Thunderbolt on the machine, but to no avail. Team Rocket advances on Togepi, Pikachu and Voltorb, causing an angered Poncho to summon a Dugtrio, which creates a massive hole underneath Team Rocket's machine, sending the trio deep underground.
Poncho tells the group that the job is only half-finished and releases all of his Diglett once more. The Diglett begin digging under the Electrode and cause them to roll into Poncho's underground tunnel. In the process, the Electrode sweep Team Rocket along with them as the Diglett act as a conveyor belt to move the Electrode back above ground. Dugtrio leads all of the Electrode out to the grassy prairie, where they jump around happily. Poncho takes Ash and his friends to the prairie in his Diglett hot-air balloon, where they watch the Electrode enjoying themselves. With the job finished, Voltorb goes to rejoin its friends and is followed by Togepi, who doesn't want it to go. However, Misty assures Togepi that it can still be friends with Voltorb, even when the pair are separated. After saying goodbye, Voltorb rushes off, leaving behind a teary-eyed Togepi.
Soon, the island is re-inhabited by people and the bridge is repaired. With the ferry service is running again, Ash, Misty, and Tracey say their goodbyes to Poncho before boarding the ship. Unbeknownst to them, a familiar Jigglypuff boards the ship as well.