How to get Epona Back
First learn how to use the powder keg, then blow up the big fat stone on milk road.(on the first day) Then go in and talk to the little girl and she let's you ride epona, for training for when the aliens come, and you just leave, and no one stop's you!
More tricks, tips and cheats for this game are right here - Zelda: Majora's Mask cheats
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