When Arceus transports most of the Pokémon to Equus, there is much panic in Stagland, Empire of Deer. The forests suddenly become feared like the Everfree in Equestria, full of creatures with potentially dangerous powers.

On this fateful day, a fawn named Ilex meets a shy pink deer named Flora. She says she came from someplace called "Unova", and was separated from her herd. Turns out that Flora is a Deerling, one species of the newly-arrived Pokémon. Meanwhile, a young boy named Tyler, from the Hoenn region, woke up in these same woods as a Pichu, along with his family's lazy house-Skitty named Coco. His older brother Jasper started his Pokémon journey the previous day, but where is he now?

Now lost and alone, these children seek to find their families. How will they grow up in this new world?