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Giant Pokémon, while rarely playing a large part in terms of plot, are nonetheless a recurring theme in the Pokémon anime. There are several episodes that have a plot revolving around unusually large Pokémon, such to the point that it seems to be a rather common mutation for Pokémon to go through.
In the anime
Ancient giant Pokémon
Several ancient giant Pokémon appeared in the The Ancient Puzzle of Pokémopolis. These Pokémon were all covered in tattoo-like marks. Gengar emerged from a black vajra-like artifact, Alakazam emerged from a spoon-like artifact, and Jigglypuff emerged from an ancient bell.
Temporary giant Pokémon
In the games
In Hey You, Pikachu! one of the activities involves Pikachu fishing, and it is possible to fish Pokémon much larger than average. There is also an Oddish that, instead of evolving, grows larger when it is watered, until it is at least ten times Pikachu's size.
In Pokémon Ranger: Guardian Signs, Hocus attacks the player with a giant Crobat when he is faced in the Sky Fortress.
In Ruby and Sapphire, there are two men living in Sootopolis City who respectively want the player to bring them large specimens of Barboach and Shroomish. Likewise, in Pokémon Emerald, the same two men want the player to bring them large specimens of Lotad and Seedot.
In the Super Smash Bros. series, the player can be temporarily large by eating the Super Mushroom. Jigglypuff's Final Smash, Puff Up can make Jigglypuff gigantic temporarily, plus knocking out any opponent near it.
In the manga
In The Electric Tale of Pikachu manga
The giant Haunter Black Fog
In The Electric Tale of Pikachu, Sabrina is attacked by a giant Haunter called Black Fog in Haunting My Dreams. Black Fog is an unusually large Haunter, that was unusual in its density and its ability to use two moves simultaneously. It destroyed itself rather than be captured by Ash.
Ash caught a giant Slowpoke in Ash vs. Gary. He later gave it to Gary in exchange for a picture of his sister, May Oak.
In the Pokémon Gold and Silver: The Golden Boys manga
In Pokémon Gold & Silver: The Golden Boys, a giant Sudowoodo blocks Route 36. It turns out that the Sudowoodo is giant because of dried mud covering its body.
In the Pokémon Adventures manga
In Pokémon Adventures, Dragonite are generally shown larger than they usually are, as with some other Pokémon.