I'm stuck in Johto and it wont let me fly or take the s.s aqua back what do I do to get back to kanto?
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There are two ways from getting to Johto to Kanto: Flying and the Magnet Train.
If you fly to Victory Road or Indigo Plateau, you can then fly to anywhere in Kanto.
If you have the Magnet Train Pass, you can take the Magnet Train from Goldenrod City to Saffron City.
Hope this helps!
Take the Magnet Train.
Walk from Viridian.
Fly to Indigo Plateau and then to Johto.
Wait for a day the SS Aqua to dock in Vermillion.
There are four ways, if none work then either your game is defective or you've damaged your game though hacking.
Did you go to Victory Road or Indigo Plateau? Maybe fly there and fly to a city/town.
For more questions for Pokemon Heart Gold check out the question page where you can search or ask your own question.
GO TO NEWBARK AND SURF ACROSS THE WATER TO KANTO, THEN FLY WITH A POKEMON WHERE YOU WANT TO GO. WORKS WHEN YOU DON'T HAVE A RAIL PASS YET