Fluttershy, long-time carer of stray Pokémon and one of six saviors of the world against Nightmare Moon, is far overdue to begin her Pokémon adventure, never having formally captured a Pokémon or registered as a trainer.

That changes after a fateful encounter in the Everfree forest, and with a foul-mouthed Bidoof at her side and some encouragement from her friends, she sets out to just secure one or two badges and call it an adventure. But the world has other ideas...