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Even before the games, alternately colored Pokémon have made occasional appearances in the anime. The first to ever appear was a pink Butterfree in Bye Bye Butterfree. Many alternately colored Pokémon appear in the Orange Archipelago due to the tropical climate. Shiny Pokémon began to make appearances in the anime during the Johto saga after Gold and Silver were released. What follows is a chronological list of alternately colored Pokémon that have appeared in the anime.
Butterfree made her appearance in Bye Bye Butterfree. Ash's Butterfree fell in love and attempted to woo her with a courtship dance. Despite this, the pink Butterfree was not impressed by his attempts and rejected him. She eventually changed her mind when Ash's Butterfree saved her from Team Rocket, choosing him to be her mate.
Butterfree in the Orange Islands have differently colored wings as well as a different wing pattern as those seen in the mainland. The first one appeared in Poké Ball Peril. It had not eaten for days despite Professor Ivy's effort to make different kinds of food for it. It took a liking to Brock's food, however, and was one of the reasons he stayed behind.
Raticate was one of the many alternately colored Pokémon that lived near Professor Ivy's lab. In Poké Ball Peril, it wondered too close to a group of Vileplume spreading Stun Spore and ended up getting paralyzed. Professor Ivy saved it before any serious damage could occur.
In The Crystal Onix a special Onix made of glass crystal appeared. It lived in a cave on Sunburst Island away from civilization. Mateo wanted to capture the Onix so that it could give him inspiration to create glass Pokémon sculptures. However, just seeing it gave him the inspiration he needed.
Rhyhorn was one of many pink Pokémon that lived on Pinkan Island were the special Pinkan Berry grew. In the episode In The Pink, Tracey took the time to observe this rare Rhyhorn and drew pictures of it. Ash upset it by approaching it and it ended up charging off a cliff. They eventually saved it with the help of Officer Jenny.
Nidoking was one of many pink Pokémon that lived on Pinkan Island. In the episode In The Pink, Nidoking attacked Team Rocket after they tried to capture a pink Nidoran♂ and Nidoran♀. Officer Jenny was able to subdue him by wrangling it with her jeep and tying him up with a rope.
Noctowl was the very first Shiny Pokémon to appear in the anime. In Fowl Play!, Dr. Wiseman was trying to capture this Noctowl using traps rather than Poké Balls, but each time Noctowl outwitted him and escaped the traps — usually leaving him hypnotized in the process. After Ash rescued it from Team Rocket, Ash had Pikachu battle it and he captured it, adding it to his team.
In A Better Pill to Swallow, Old Man Shuckle sought out this Shuckle for its ability to create a special juice that was necessary for a special medicine to ensure Pokémon obedience. However, Team Rocket got hold of the Shuckle and drank its juice pure, which had the effect of making all nearby Pokémon obsessed with them. Old Man Shuckle was able to cure this by throwing a powder at them that apparently acted as an antidote.
Magneton made its sole appearance under the ownership of Jackson, in Tie One On!. It proved to be very powerful and strategic. Jackson sent it out to battle Ash's Pikachu. After a long battle, Magneton finished Pikachu off with a Tri Attack, then went on to defeat Cyndaquil without a problem, before finally falling to Bulbasaur.
This Magikarp made its sole appearance in a flashback occurring in Judgment Day! In it, Jimmy found himself briefly in possession of the Magikarp, before someone who suspiciously resembled the Magikarp salesman offered to trade his Charmeleon for the Magikarp, a trade Jimmy accepted.
Donphan made her appearance in Date Expectations, which took place during the Donphan mating season. She was the target of the attention of a number of male Donphan, who all attempted to impress her by using Rollout. However, it was an injured Donphan who won her over, with a little help from Ash and his friends.
Metagross made its sole appearance in Noodles! Roamin' Off!. After Jessie, James, and Meowth had disbanded, James went after this Metagross, with the intention of presenting it to the boss and crediting the whole trio, believing the promise of success to be enough to bring Jessie and Meowth back. However, James was unaware that this particular Metagross was notorious for its vicious temperament and its reputation for injuring all challengers. Once Jessie learned that James was going after the Metagross, she and Meowth rushed to his aid. This was well-timed, as James, Mime Jr., and Carnivine were all tied up by Carnivine's own vines, and about to be finished off, Seviper and Yanmega came to the rescue, knocking Metagross into a canyon. Ultimately though, Metagross sent Team Rocket blasting off with a powerful Gyro Ball.