I'm a big fan of Pokemon and MLP so most stories will be crossovers of the two. I am also a big fan of Valve, so I might make a crossover or two with the valve universe.
Equestria is at war with the Pokémon world. Celestia is trying to rid Equestria of all Pokemon except for Twilight and her friends Pokemon. Quilava knows that if nearly every Pokémon is removed from Equestria nothing would be able to stop the ones left if something went wrong. He hopes that this could be solved peacefully but after the death of a close friend he's out of mercy.
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My Little Pony: Friendship is Magic Fanfiction
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So, uh.
Hm.
If the conflict is Equestria vs the Pokemon world, it isn't really a civil war, is it? It's just war, assuming that the appropriate parties have made the necessary declarations to elevate it above being a skirmish or a police action. I guess Ponymon: Police Action doesn't really have that same Marvel tie-in, though.
Could... Could you add Rayquaza, and, and other dragon Pokeemons?!