Due to Lord Arceus' plan to transfer the Pokemon and all worthy humans to Equestria, Skye, Hiro and Jewel are separated. Skye finds herself in the company of a group of ponies who ran away during Sombra's evil reign. Hiro lands deep in the Everfree forest. However, he does not trust the ponies of Ponnyville and hides in the Everfree. Jewel is stuck within the Changeling Empire, under the care of a loving family. However, she longs for Skye and Hiro.

Will the two, and more, be able to find Skye to lead them into the future, or will they be separated for the rest of their lives?