Mystery at the Lighthouse (Japanese: でんげきたいけつ！クチバジム Bill's Lighthouse) is the 13th episode of Pokémon: Indigo League.
Ash gets depressed after hearing that his previous achievements were just hollow. He manages to capture a Krabby, but sees that the Poké Ball disappeared. Learning that he can have six Poké Balls in possession, he wants to learn if Professor Oak is taking care of it. The heroes go in a nearby lighthouse and meet Bill, who tells them of a mysterious Pokémon. Will they see and hear this mysterious Pokémon before Team Rocket decides to get it?
Ash, Misty, and Brock were walking through a forest. Ash started bragging about how he had caught the three starters, when Misty said that he hadn't caught any of his Pokémon, his Pokémon decided to follow him. This got Ash really mad and he ran through the forest swearing that he would catch his 7th Pokémon, only this time for real. When Ash got to the end of the forest, he found himself on a small beach. While Ash was trying to think of what Pokémon to catch, he saw a small Krabby running around his feet. Ash threw out a Poké Ball and caught it easily. The Poké Ball suddenly transferred to Professor Oak's lab. Ash became frantic about where his Krabby had gone. Brock and Misty come out of the forest and ask Ash what he is doing. Ash responds that he is looking for the Poké Ball that he caught Krabby with. Misty informs him that a Pokemon Trainer can only carry six Pokémon at a time. The other Pokémon get sent to Professor Oak's Lab. Suddenly, Pikachu started jumping up and down and pointing at a building in the distance. They all look over at it a realize that its a lighthouse and they all race towards it.
By the time they had gotten to the lighthouse, it was dark out and the long walk to the lighthouse had worn them all out. Ash ran the bell and someone said, ""Who's there?"
After Ash and his friends explained their situation and Brock offered to cook the lighthouse keeper a cheeseburger, they were let in. As soon as the door opened, they noticed that no one was there to greet them. Ash asked out loud is he could use the lighthouse's phone and they heard someone say, "Yes, there's a phone right near you". They still didn't know who the lighthouse keeper was.
Ash called Professor Oak about his Krabby and Professor Oak is shown on the phone's screen cooking dinner. Ash gets worried, thinking the Professor is cooking Krabby. Professor Oak assured him that Krabby was safe. Professor Oak showed him the Krabby that Gary had caught. Ash got mad because it was way bigger than Ash's. He went crazy when Professor Oak told him Gary had caught 45 Pokémon while Ash had caught only 7. Professor Oak told him that he is calling from Bill's Lighthouse and that Bill knows more about Pokémon that Professor Oak, so it would be a good idea to listen to him. Ash says good bye and hangs up the phone.
Suddenly, a giant Kabuto appeared, saying that it was the keeper of the lighthouse. Elsewhere, Team Rocket was outside the perimeter of the lighthouse and they decide to steal everything in there. They decide to climb the cliffs, and then they recite their motto. Meanwhile, The Kabuto said that his name was Bill and he got stuck inside the Kabuto suit during a research project. Ash, Misty, and Brock help Bill get out of the Kabuto suit. Bill thanks them and tells them that there are 150 different kinds of Pokémon, something Ash didn't know before. Bill also explained that there are many more Pokémon yet to be discovered. He also gave Ash a few things to think about, like "A Meaning for All".
Outside on the cliffs Team Rocket is still climbing the cliffside. Jessie was contemplating on the meaning of it all. Bill says there is one Pokémon he is searching for and it was the biggest Pokémon he had ever seen. He said it was unique and that no one had ever seen it before. He said that one night he had heard a strange noise coming from across the lake and the Pokémon had made the noise. Bill said that was the last time he saw the Pokémon.
They all heard a strange sound and a large Pokémon rose out of the lake. Bill said it was the Pokémon he had heard before. As the Pokémon came closer, they realized that the Pokémon was a Dragonite. The Dragonite came closer and Team Rocket was shown climbing the cliff. When they saw the Dragonite, they started launching missiles to try to catch it. Dragonite got mad and swung his tail at the trio, causing them to fly off into the distance. The Dragonite started to walk away, Bill tried to call it back but it didn't listen.
In the morning, Bill didn't appear upset that the Dragonite had left. He was happy that he just got to see it. With another lesson from Bill, Ash, Misty, and Brock leave the lighthouse waving Bill goodbye.
- "That's right Brock, in the league, a trainer is allowed to carry six Pokémon at a time. What are their names again Ash?" - Narrator
- "Their names are:" - Ash
- "Pikachu." - Pikachu
- "Pikachu, Pidgeotto, Butterfree, Bulbasaur, Charmander, Squirtle, and I caught them all, fair and square." - Ash
- "Caught them? Ash, all of your Pokémon followed you." - Misty
- "You're always putting me down, but I'll show you! I'm gonna prove to you I can do it! I'm gonna be a Pokémon Master. Stand back and watch me work." - Ash
- "According to the phone book, that lighthouse belongs to Bill, the famous Pokémon researcher." - Jessie
- "Then I guess we've come to the right place, huh?" - James
- "How shall we sneak in? We could take the road, or risk our lives by climbing up the cliffs." - Jessie
- "Well we certainly can't take the road." - James
- "We have to climb up those cliffs." - Jessie
- "Cause we're the bad guys, and the bad guys always gotta sneak in." - Meowth
- "To be truly great criminals we have to do things the hard way." - Jessie
- "And then we'll become hardened-criminals." - James
- "But it will be tough to reach the top..." - Jessie
- "...cause we're afraid of heights!" - Jessie and James
- "It sounds like it's singing." - Misty
- "Would you care to dance?" - Brock
- "Oh, thank you." - Misty
- "What beautiful music." - Jessie
- "It's very haunting, yet so sweet." - James
- "Quite right. I'll attack it at once. But it seems a shame to aim at such a sweet creature." - James
- "Of course it's a shame, we built our fame on shame." - Jessie
- "Go on fire! It's all the shame to me." - Meowth
- This is the first episode that sponsored 1-800-Collect.
- An image of Mewtwo can be seen on the lighthouse's door.
- Bill's chart had all the Generation I Pokémon except Mew. The ones Ash obtained had a red dot over them: Pikachu, Pidgeotto, Butterfree, Bulbasaur, Charmander, Squirtle and Krabby.
- Bill was voiced by the late Maddie Blaustein.
- At the beginning of the episode, the narrator breaks the fourth wall by talking to Brock and the others.
- The "Who's that Pokémon?" is Krabby.
- The mysterious Pokémon is a secret.
- When Meowth was talking how to get into the lighthouse, his ears were teal.
- Misty said to Ash that the Pokémon he obtained were following him, but this was incorrect because Pikachu was given to Ash by Professor Oak, Butterfree as a Caterpie was a lucky catch, Pidgeotto and Bulbasaur were captured in a legitimate battle, while Charmander and Squirtle were the ones who followed him.
In the original, after Jessie says that she, James and Meowth should climb the cliff to the top to reach the lighthouse, they question themselves weather or not they can, while in the dub, it's ironically revealed that both Jessie and James are afraid of heights.