Obscure Hunts
These shiny hunts are some of the least known shiny hunts, with few people knowning they can be completed, some of these hunts may not have even been intended, meaning that the pokémon obtained in this way are quite special.
Generation One Trade Pokémon
Similarly to other generation one Pokémon, Pokémon recieved in a trade can be shiny, these Pokémon are also unique in that the level of the traded pokémon is determined by the level of the pokémon you trade to them, this means that trade pokémon can be obtained at a high enough level to check their DV's to ensure that they will become shiny when transferred.
Click here for a list of obtainable trade Pokémon
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Extreme Speed Dratini
In generation two there is a special Dratini that can be obtained by answering a set of questions correctly in the "Dragon's Den" This Dratini knows the move Extreme Speed and can also be shiny, after answering the questions correctly you are able to save the game before accepting the Dratini, which means that it is not required to answer the questions correctly every time.
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Wild Wynaut
While Wynaut itself is easily obtainable through eggs, wild Wynaut are much more rare, only being found on the ilusive "Mirage Island"; an Island that only appears if the first two bytes of a Pokémon's personality value match a random number between 0 and 65536, if all of a players Pokémon have different ID's, then this results in a 6/65536 or 1/10923 chance of mirage island appearing, Wyanut is the only Pokémon found on this island and is only found on Mirage Island, this means that this is the only way to get a Wynaut in a ball other than the standard Poké Ball.
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e-Reader Shadow Pokémon
As an extension of shiny shadow Pokémon's rarity, a set of e-Reader cards compatible with Pokémon Colosseum were released only in Japan, these e-Reader cards could then be scanned to access three new shadow Pokémon, Mareep, Togepi and Scizor, these shadow Pokémon can also be found shiny and for specifically Scizor, is the only way to get a shiny Scizor with the National Ribbon
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Sinjoh Ruins Creation Trio
In Pokémon Heart Gold and Pokémon Soul Silver, there is an obscure event invoving the Pokémon Arceus that takes place in the Sinjoh Ruins, this event allows the player to get one of the creation trio at level one, in a Poké Ball holding their respective orb, this Pokémon can be shiny and this event can be done twice, meaning two of the three creation trio members can be obtained in one save file, this event is no longer possible without glitches or fan-made external systems which replicate events that were given out, as Arceus was only ever distributed as an event.
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Hall of Origin Arceus
A peculiar case as this is the first Pokémon that is obtainable without the use of external devices, yet is still barred entry to the newer generations, the event used to access the Hall of Origin was never released, leaving the Arceus obtained there Inaccessible, this Arceus is still obtainable using the void glitch, or through the use of Arbitrary Code Execution to obtain the unreleased event item, this Arceus is able to be shiny and can also be used for the previously mentioned Sinjoh Ruins event as the hack checks introduced in later generations are not present in local trades, nor did generation 4 have any hack checks itself.
Link to a guide on obtaining Hall of Origin Arceus using the void.
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Zoroark
Zoroark in generation five is one of them most unique Pokémon in the series, it is one of few non-mythical Pokémon that has been locked behind an event, it is the only in-game event actived by an event Pokémon from a previous generation and it is the only event that restricts access to a TM in game, likewise it has one of the more unique shiny hunts in the series, initially when encountered Zoroark will be disguised as either Entei, Raikou or Suicune, after taking direct damage, this disguise will vanish, strangely the game will roll for both Zoroark and the disguised legendary beast to be shiny separately, this means that if the legendary beast is shiny, as soon as the Zoroark is damaged that shiny lost forever.
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Trash Can Rotom
Generation six added a new way for Pokémon encounter tables to be decided, this being based on the current day, day-specific Pokémon was combined with existing rock smash encounters to create trash can encounters, on certain days, Rotom may be found in the Lost Hotel by checking trash cans on tuesday, while not as complex as other hunts mentioned, it is still equally as obscure
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Partner-Cap Pikachu
Introduced in Pokémon Ultra Sun and Pokémon Ultra Moon, Partner-Cap Pikachu can be obtained in Pikachu Valley, this Pikachu has a different OT than the player and however this Pikachu is shiny locked to the players shiny value (TSV), because of this there is a 1/4096 chance that the shiny lock will function correctly, in every other situation this Pikachu can be shiny, this Pikachu was never intended to be shiny and was never given a shiny colour, however due to this glitch never getting patched, this Pikachu is recognised as legitimate and can transfer to newer generations
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Ditto
In generation seven there is a side-quest involving five Ditto causing trouble in Konikoni City, all of these Ditto are able to be shiny and have fixed stats, this city has very little relevance to the story of these games, making it incredibly easy to miss this event, more Pokémon are available in a similar way and can all also be shiny, some of these include Gastly, Drifloon, Sandygast, Frillish and Pinsir.
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