An Undertale crossover.
When Asriel breaks the barrier and frees all the monsters from the Underground, he stays behind, knowing that soon, he won't be able to maintain his form, turning back into a flower.
But Frisk won't accept that, no matter what he says. After countless tries, he finally gets Asriel to accept his soul, fusing both of them together and saving Asriel from life as a flower.
But when Frisk tries to load a save, things get a bit glitchy, and they are thrown from the dimension to resolve the paradox.
Disoriented and spinning in the space between worlds, they attempt to return to their own. Instead they find themselves in Equestria just before Nightmare Moon's return.
Note: Frisk and Chara are often considered "genderless" by some, since Toby Fox said that they were intended to be assigned a gender based on the user's choice. For this story, I have decided to make Frisk male, mostly for the convenience, and to avoid the "changing genders" dilemma. (I made Chara female, but that really doesn't matter all that much for this story.)
Also, I would like to direct you to a neat little comic series called A Dreemurr Reborn. It is based on a similar premise (although without MLP). There was a bit of influence for this story, although I had this idea way before I saw that, back when I first played the game.
Yeah, I know the hype for Undertale has died down by now, but so has the hype for ponies. I don't really care. 
