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Because they say a boy (I guess Red) stopped Team Rocket in the past and now they've come back.Also you see Red in MT.Silver, and the Elite Four is changed, Lance is the champion, Blue is the 16th gym leader, and Giovanni is gone.

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It is not, actually. It was a remake of G/S/C.

>Much like how Pokémon FireRed and LeafGreen revisited the Generation I story of Kanto, HeartGold and SoulSilver retell the story of Johto, with the player's starting town being New Bark Town. -Bulbepedia

I guess they put different gym leaders to make it more interesting.

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Actually, G/S/C is a continuation of R/B/Y, and the same for the remakes.