PokéBase - Pokémon Q&A
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For example, I trade a Zangoose from Black 2 to Omega Ruby using the PokeBank. The OT (original trainer name), ID and Secret ID on both games are exactly the same, which, under normal circumstances, would have the Zangoose act like a Pokemon I caught on my own, obeying every command and not gaining extra EXP. However, there is a generation gap, the game will say that it came from Unova. Will the Zangoose get the boosted EXP and act as an outsider Pokemon, or will it act like I never transferred it in the first place and obey my every command if I'm missing badges?

This can be asked about any trading between any generation, like gen 1 to gen 2, gen 3 to gen 4, gen 4 to gen 5, etc.

(Yes I know the chances of this happening are slim to none, I'm still curious.)

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Don't make the same mistake I did; the name still has to be the same lol.
Just remembered that lol, thank you
Theoretically, when a Pokemon is traded, its location will state which region it came from. Since intergenerational migration  If the Pokemon is traded between a pair of identical games (in terms of trainer name, IDs etc.) that share the same region, the location would not raise a red flag in this case. However, your question brings up intergenerational migration which would usually have a different region. This should distinguish the Pokemon's true origin, therefore it should be treated as a traded Pokemon. I don't want to answer unless you're happy with it but you know

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It will act as a traded Pokemon because of the region difference. Also Pokemon don't have secret IDs, only trainers. Any difference at all is enough for it to be a traded Pokemon. This is only for 6th gen though. I don't know about past generations.

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