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It won't let me fly from kanto to johto in Pokemon silver. I flew to Indigo Plateau and the only places I can fly is in kanto. Why?

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In the original Gold/Silver/Crystal, you are unable to fly between Kanto and Johto. This is only possible in the remakes. The only way to get between Kanto and Johto in the originals is through either the magnet train or the S.S. Anne.

Source: experience

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There is one other way, which is to cross routes 26/27 manually, but that's pretty unwieldy unless you're going east (from New Bark Town, you can surf 3 tiles into the water and then you can Fly to Kanto locations)