The show begins with Ash, Misty, and Brock lost again. Ash is feeling proud of himself as he has six Pokémon and two badges. Misty and Brock bring him down to earth by telling that he didn't catch most of his Pokémon, they chose to follow him. Misty goes on to say that he truly didn't earn either of his badges, as he didn't actually defeat either Brock or Misty in a battle. All of this makes Ash depressed, and he runs ahead of them.
He suddenly comes upon a beach and realizes that he's finally out of the woods. The sunset is beautiful, but he focuses his attention on a small Krabby that crawls by. He decides to catch it, to prove that he can do things on his own. He weakens the Krabby single-handedly, and catches it.
In a flash, the Pokéball disappears and Ash is instantly worried. Brock and Misty show up and explain that he can't carry more than his six Pokémon and the Krabby was transported to a place of safe-keeping, namely, Professor Oak's lab. Ash is even more concerned, as he doesn't exactly trust Professor Oak, and he wants to call him. They see a lighthouse on a cliff and Ash is eager to call the Professor from there. Misty is eager to sleep in a real bed, and Brock is eager to make some real food.
They dash the longer-than-it-looked path to the lighthouse and stop at the entrance to the building. The two doors are huge and covered with etchings of Pokémon. They ring the doorbell and are let in by the lighthouse's keeper, Bill. They start to explore, but Bill is nowhere to be found. Ash finds a phone and places call to Professor Oak where he sees that his Krabby is in good hands. His Krabby, however is puny compared to Gary's and Ash is upset to find out that Gary has already caught more than 40 Pokémon, for he only has seven. When the Professor asks where Ash is calling from, he describes the lighthouse. Professor Oak recognizes Bill as a well-known Pokémon researcher and tells Ash to talk with him. Bill appears, and Ash and his friends are astounded to see that he is a Kabuto.
Bill explains that he is not a Kabuto, but he is stuck in a Kabuto costume. Ash helps him out, and they start to talk. Bill explains that he looks for rare Pokémon to study and learn more about. He goes on to say that quite a few months ago, he heard the cry of a huge monster from across the ocean. He recorded it and as been playing it back in hopes of bringing the Pokémon to the lighthouse. When Ash asks if he wants to catch the it, Bill says no, replying that he only wants to meet it.
We find Team Rocket sneaking around the lighthouse, planning on stealing the rare Pokémon that they are sure Bill has stored there. In order to take him by surprise, they scale the cliff the lighthouse is on, instead of taking the road up to it.
Suddenly, everyone hears a song in the wind. The Pokémon Bill has been waiting for has finally come. Bill starts up his recording again and turns on the beacon to draw the monster closer while Brock and Misty start to dance to the music. Team Rocket, on the other hand, upon seeing the creature, decide to catch it. They pull bazookas from out of nowhere and start firing.
The Pokémon is furious and, in its rage, smashes the beacon and knocks Team Rocket from the cliff. Bill beseeches the creature to stay, but the Pokémon shakes its head, turns, and heads back out to sea. He is saddened to see the creature go, but is happy that he was at least able to see it.
After receiving some words of advice and encouragement and a reminder of the sheer number of Pokémon to be found, Ash, Misty, and Brock continue their journey to Vermillion.