PokéBase - Pokémon Q&A
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What "little windstorm of thunderstorm" thing?
When you are in the same area as Tornadus or Thundurus there is a violent storm that signals the presence of that pokemon, but only so with those two.

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No it will not, being as that only happens in the story mode when they are Roaming, not Post Game when they are not.

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No, beacause that storm only happens when they are roaming, if you hack it they aren't roaming.

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