Mewtwo was tired of fighting. That's all he ever got to do. Fight. He was sick of it. Considering how lonely he was, he was surprised to keep being found by good and evil. In the end, both sides used him as a tool. It sucked.
Now, Mewtwo hid in the heart of Equestria in Manehattan, where no one would care if a pony stuck out.
Yes, Mewtwo temporarily changed himself into a pony when he needed to buy things. So what?
In the meantime, Mewtwo was hungry, so he always had a box of waffle mix. He was going to make pancakes, but why not waffles?
When he began to sit up to make himself some breakfast, he was pushed back into bed.
"What the hell" Mewtwo thought. The hoove which held him down was firm, intentionally keeping itself on his chest.
It was a black, with a blue glow to it. Beside it, beautiful hair sparkled in dark colors. Mewtwo was mesmerized by it.
Mewtwo looked up. A face was hidden by shadow, fake shadow.
"I have a preposition for you" the face said, not yet revealing its identity.
"Who are you" Mewtwo asked. "Why are you here?"
The figure leaned in. Mewtwo had seen her before, but couldn't remember where.
"I'm Nightmare Moon" she said, "like I said, I have a preposition for you."
"Which would be" Mewtwo asked, puzzled by what was happening.
"As you know, you are wanted by everyone, and it must be annoying running away all the time" Nightmare started,
"Considering how powerful you are, you would make a great addition to The Dark Council, which, if you joined, would make sure you were hidden, never to be found by Equestrians or humans, as long as you do as I say".
"What kind of things would you ask me to do" Mewtwo asked, gazing into Nightmare's eyes.
"Oh, just simple scrimmages for more territory, after all, Equestria is in chaos" Nightmare answered.
"That's it" Mewtwo said.
"That's it" Nightmare said.
Mewtwo pondered on it.
He had never actually joined a government council, and it sounded good.
"I think I might just do it" Mewtwo finally said, thinking of the beauty of Nightmare Moon.
"Excellent" Nightmare said, "Lets go see if the Council thinks your worthy enough to join.
And they left.