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...And which Pokemon first received this treatment?

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Wait wuh? Just make that a new question and keep this one
Sorry, accidentally edited this question instead of making a new one. It's back now. Lol
I edited my answer a little

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The first main-series game to have a different piece of music when battling legendary Pokemon was Crystal. However, I'm pretty sure that the only time that this music was played was when battling Suicune.

Sources: The track listing comment this YouTube video, as well as the track listing comment on this YouTube video.

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didnt raikou and entei have exlusive theme in gold and silver?
As far as I know, no.