Lord Arceus, the creator of the Pokémon universe, had enough of humanity's use of the Pokémon as tools and decided to escort the Pokémon and a few now-former humans of his choice to Equis to live their lives in peace.

But what they didn't know was that there was the mysterious Q continuum, always watching, they were capable of hiding themselves from even Arceus.

But now they decide to show themselves. The fate of Equestria's changed forever.

Who are these strangers? Why is Discord connected to them? Why isn't he aware?

Those mysteries will be uncovered in time.

Note: The story starts during Chapter 2.2, so the mane six aren't going to be on the ride for the first chapter or so. Pokémon from Gen 7, notably Solgaleo and Lunala, will come later on.
Note: Yes, Discord is Q. But with a twist I'll explain later on.
Note: I know of the max three rule, but there will be more than the MLP, Pokémon, and Star Trek.