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>Articuno, Zapdos, Moltres
Regular legendaries, but there are more than three. Since you can find them in Hoenn (via mirage spots), Sinnoh, Alola (via wormholes), and Kalos. Not to mention some Frontier trainers have them in Emerald and Platinum. Few left in existence, but can probably breed.
>Mewtwo
Legendary, but there are 4different instances where you can catch one. Kanto, Kalos, Hoenn, Alola. Head cannon I guess would be that it’s a lab experiment, so formulas and shit can be replicated.
>Mew
Only one instance in the games where you can actually catch one and that’s in Emerald via faraway island. Probably the last Mew in existence.
>Raikou Entei Suicune
I don’t even fucking know about these three. The lore is supposed to be that three Pokémon were killed in one of the Ecruteak towers, Ho Oh then revived them and made them legendary beasts. But why the fuck can you find more than those three in Kanto, Hoenn, and Alola? I guess you could say perhaps one of the dogs roamed beyond Johto and into Kanto. Sure. But what about the ones in Hoenn and Alola?
Maybe mirage spots are like portals to the Pokémon’s native region and you’re essentially catching them and taking them away from their home. Wormholes must be the same deal because I don’t know how else to explain it.