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Actually I believe you do have to defeat the aliens, because you technically can't call Epona until after you do fend them off. Correct me if I'm wrong though, I honestly can't remember completely.

Yeah, if you try modding, or use the Crooked Cartridge glitch, but neither are very wise to try to use, and they are cheating. It's pretty much inevitable that you need to get your horse in order to proceed to the third dungeon.