This story is a sequel to Ponymon: Threats From Another World

After an argument, Twilight tries to reconnect with the Pokemon world so she can get Quilava to answer her question. She succeeds but brings three powerful Pokemon into Equestria Mew, Mewtwo, and Hoopa. A misunderstanding with Mewtwo causes him to get angry and he flees. Hoopa goes after Mewtwo, but both Pokemon are mind controlled by a stallion known as Sombra. He make Hoopa summon several legendary Pokemon to aid him in conquering Equestria. All that stand in his way are Mew, Twilight, Quilava, Rainbow Dash, and Latios.