The Mystery is History (なぞのポケモンＸ！！ Mysterious Pokémon X!!) is the 11th episode of Pokémon: Master Quest.
On an island near Silver Rock Isle, Ash and co are reunited with their old friend Ritchie, who they haven't seen since the Indigo League. After they catch up, Ritchie tells them he's been on the lookout for the Mystery Pokémon of the Whirl Islands. They soon encounter a young boy named Oliver who was playing with an unusual Pokémon, a Lugia. However, it was much smaller and Oliver nicknamed it Silver. Eventually, they meet their old friend Luka, who takes them deep sea diving and find the child's parent. But are they the only ones interested in Lugia?
As soon as they encountered Sparky, the heroes find Ritchie as well, who is glad to see them. The heroes see that even the Pikachu and Togepi are glad to see Sparky. Ritchie came to the island to witness the mysterious Pokémon, which the heroes are looking for as well. Ritchie tells he did research, but many sources claim other facts. Ash confesses he saw the mysterious Pokémon near Blue Rock Isle, but saw a shadow of it. Nevertheless, they see it brought them together and think the mysterious Pokémon is nearby. Ritchie points at a deserted isle where that Pokémon might be, so they take a boat to get there. A boy plays with a Lanturn and a Pokémon named Silver. Upon seeing the heroes, the boy orders Silver to hide from the people.
The heroes ask the boy if he lives here. The boy confirms and introduces Lanturn and himself as Oliver. The heroes ask if he saw the mysterious Pokémon, but Oliver claims he never saw one and thinks they should look at other islands. Ritchie asks what about the other Pokémon he saw, but Oliver claims he only has Lanturn and bids the heroes farwell (although nervously). While the heroes hoped for some info, Ritchie thinks something is not right. Oliver is pleased the people went away and hugs Silver. Some Team Rocket members spy on Oliver. In an underwater base, the members contact Dr. Namba and show him the boy and the Pokémon. Namba recognizes it to be Lugia. A Team Rocket member asks for his order, so Namba wants fishsticks. The member clarifies what are his orders about Mysterious Pokémon X, so Namba orders it to be captured, but must be unharmed.
The spies use nets to capture Silver. However, Lanturn tackles the spies, so Silver is saved. Oliver rides Lanturn to get Silver somewhere safe, but a submarine appears before them. The heroes search for the mysterious Pokémon, but find nothing. Ritchie tells them he thinks Oliver was hiding something. Jessie, James and Meowth spy on the heroes and plan on capturing the two Pikachu. Suddenly, Team Rocket and the heroes see Oliver riding Lanturn with a Lugia, trying to save it. The heroes see Oliver being chased by a submarine, so the heroes know Team Rocket are the ones chasing Oliver. However, Butch and Cassidy appear out. They release a net to capture Silver, but Ash sends Lugia, whose Razor Leaf cuts the net. Cassidy sends Houndour and Butch Hitmontop. Houndour uses Flamethrower, but misses, though Hitmontop's Rolling Kick hits Bayleef. Ritchie sends a Pupitar named Cruise, who takes down Hitmontop. Houndour uses Flamethrower on Cruise, but it does not seem hurt.
Hitmontop uses Triple Kick, but Bayleef's Vine Whip causes Hitmontop to be reflected back, hitting Houndour instead. Butch and Cassidy call Houndour and Hitmontop back. Butch and Cassidy go to capture Silver, but the submarine gets hit by Luka's ship. Butch and Cassidy retreat, promising to be back, while Jessie, James and Meowth follow them in their Magikarp submarine. Luka comes and shows her Silver Wing, but Brock thinks she came to see him. Ash remembers he encountered a Lugia on Orange Islands. Brock knows Lugia are supposed to be bigger, but Oliver tells it is still young, as same age as he is. Oliver admits he lied Lanturn was his only Pokémon. The heroes understand he wanted to keep Silver as a secret from people like Team Rocket and decide to keep that a secret. Ash asks if he caught it with a Poké Ball. Oliver tells when he was playing with Lanturn, a storm came and swept them. When Oliver woke up, he saw Silver, but its parent as well.
Oliver tells that it is said Lugia's parent is never far away. With that, a Lugia appears before them all, while Luka's Silver Wing glows. It looks angry, but everyone manages to persuade it they never came to hurt it. Lugia calms down, so Luka's Silver Wing stops glowing. Lugia and Silver dive underwater, so Ash proposes to go after them. Soon, the heroes, Ritchie and Oliver, dive to witness Lugia and Silver. They see Lugia feeds Silver, who also bumps into Ash. Luka sees her grandfather's Silver Wing was a feather from Lugia. Jessie and James enter the underwater base in black unifroms (with Meowth under James' uniform). James asks why do they need to wear it, so Jessie thinks they can join in the plan of capturing Lugia, then take credit for it after they present it to the boss. Butch and Cassidy report to Dr. Namba and tell them Lugia is still out there.
Jessie and James come to Dr. Namba, who wants Lugia to take advantage of its power, turning that power into a beam. Namba also asks for food, so Cassidy points at a Team Rocket member (who is Jessie) to bring them food. Outside the lab, Jessie outrages, seeing she has to serve her enemy. Jessie plans on capturing Lugia under Cassidy's nose. The heroes see that Lugia and Silver go to get more food. Ritchie wonders if Lugia spend more time in water or on land, so Brock responds they only come on land if they raise their children. Luka sees she is low on food and firewood, so tells the heroes she will be gone for a few hours to get those supplies. As the heroes have a break, a Lugia appears. Silver goes to it, but Ritchie warns that is a fake one. Silver gets captured in a cage, as Butch and Cassidy emerge from the submarine. However, Jessie and James go out of their own submarine as well, who plan on taking the Lugia to the boss. Jessie and Cassidy annoy each other, then send Houndour and Arbok.
Arbok uses Poison Sting, but Houndour's Flamethrower negates the attack and burns James, Jessie and Meowth. The heroes go to save Lugia. Butch and Cassidy go to get the cage using a robotic arm, but the arm gets destroyed by Bayleef's Razor Leaf. Hitmontop uses Rolling Kick on Bayleef, who retaliates using Vine Whip. Butch calls Hitmontop back. Houndour uses Smog, then Cassidy calls it back. Using a robotic arm, Butch and Cassidy take Silver away, then move out, causing Jessie, James, Meowth and their submarine to sink down. The heroes see Silver is taken away to the depths.
- The "Who's that Pokémon?" is Spearow.
- Ash mentions encountering a Lugia in the Orange Islands during the events of Pokémon 2000.
- Despite being a Legendary Pokémon, there are clearly multiple Lugia, as the adult one seen here is not the one encountered in Pokémon 2000.
- For the first time, Jessie and James wear the standard black Team Rocket uniforms instead of their apparently unique grey uniforms. They quickly switch back, however.
- This is the first plot where Team Rocket has a greater role.
Ritchie's Pupitar, Cruise, used Take Down, a move it cannot learn.