They came out of nowhere and launched a sneak attack on Equestria as an alien race called the Davier a highly advanced alien race with advanced Medical research and Technology along with highly trained soldiers abduct the contry's citizens for research and experimentation. They capture the Main 6 and many innocent ponies and stallions and take them into space. Leaving the Equestria defenseless and wishing for salvation to save them from these invaders.

In another dimension the Pokémon World where no humans exist a young, kind, brave, and a big dreamer Turtwig along with a young smart, brave, and kind Charmander try to join the Braviary Guild. But ends up getting spooked by 2 Pokémon and ends up in a forest and meets a lost Piplup who saids to be a human, but has amnesia and can't remember his past. When they return to the guild they create their own Exploitation Team called Team Typhoon. Later they meet Shining Armor who is now the Mythical Pokémon Keldeo thanks to a transformation spell that the 3 remaining Princesses of Equestria did on him and sent him to the Pokémon World to save Twilight and her friends along with the other ponies and stallions that were captured and joins the young team. But our young Pokémon heroes will have to face the Davier and free the Equestrians that they captured and can Piplup and his 3 new friends find out his memories of his past, unravel the Davier's mysterious agenda, uncover the connection with Terra and Earth with the Legendary Pokémon Solgaleo and Lunala, and save the Pokémon World from being concur by the Davier.

Watch as Team Typhoon battles powerful outlaw Pokémon, uncover the mysteries of the Legendary Sun and Moon Pokémon, make new friends, make alliances with 4 teams including Team Poképals and the Rescue Team called Team GoGetters including a team of humans who are now Pokémon from our world, and fight to save not only their world, but 3 different dimensions of Earth and Terra from being taken over by aliens! Prepare for the biggest battle in Pokémon history! As these new teams explore and fight to save the final frontier!

Takes place after Season 7 of MLPFiM.
All the Pokémon from all the generations are in this story.

Pokémon and Pokémon Mystery Dungeon are owned by the Pokémon Company.
MLPFIM is owned by Hasbro.