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>Mew can be obtained on Faraway Island in Emerald or as a reward in My Pokémon Ranch and got Mewnium Z
>Celebi can be obtained in Crystal with the GS Ball event or transferred from the Japanese (and is even present on the English) Colosseum bonus disc, and a fateful encounter Celebi unlocks the Giovanni event in HGSS and a Zorua in BW
>Deoxys can be found on Birth Island in FRLG and Emerald, in space at the end of the the Delta Episode in ORAS, transferred from Guardian Signs, and there have been meteors to change its form in every game since DP
>Phione can be bred from Manaphy
>Manaphy's egg can be obtained from any Ranger game and has a special appearance, and Manaphy can be seen in the Celestic Town book
>Darkrai can be obtained in the Sinnoh games from the Newmoon Island event or transferred from Shadows of Almia
>Shaymin can be obtained in the Sinnoh games from the Flower Paradise event or be transferred from Guardian Signs, and the Gracidea has been available in every game since Platinum
>Arceus can be obtained in the Sinnoh games from the Hall of Origin event, and there's a guy in Oreburgh Mine who comments on a fateful encounter Arceus in your party. The Hall of Origin Arceus and fateful encounter Arceus both unlock events at the Sinjoh Ruins in HGSS, and Arceus got a Fairy form later on
>Victini can be found in BW at Liberty Garden Tower and has a special interaction there in B2W2
>Keldeo has the Moor of Icirrus in BW and Pledge Grove event in B2W2 and Resolute Form, and can be tutored Secret Sword by someone in every game after
>Meloetta has a tutor in every game that'll teach it Relic Song
>Genesect has the P2 Lab thing in Gen V and gets drives in every game
>Diancie distributions in XY have the scene with the guy who asks you for it, while ORAS ends it with you getting Mega Diancite
>Hoopa has someone in XY to tell you more about it after showing it to him, and gets the Prison Bottle from the Poké Mart clerk in ORAS for Hoopa Unbound