Mind you this idea isn't 100% perfected.
I actually had a my little pony (human) idea. The Discord from human world sees her come out of the portal from ponyville, going in on his own. He discovers his powers and goes into hiding. The pony world discord thought he felt something but lets it go.
One day the mirror between worlds disappears. The (human) Discord uses his power, with the combination of the mirror to try and break the seal between worlds. In the human world, Human Twilight had moved back, meeting the other girls who all took on to liking her quickly. However she is rather shy trying to keep to herself. When strange things keep happening, as windows between the worlds keep giving people flashes.
Pony twilight, is called to Princess Celestia who informs her of the strange going on when suddenly the Human Twilight falls out of the principle Celestia's office through a portal into the pony world, Keeping her human form. Everyone seems surprised as Twilight is put in charge of watching over her, taking her back to her castle. Human twilight can't believe it, but gets wrapped up in her amazing library as Twilight is embarrassed about it, her friends keep crowding the human twilight, much like their human counterparts.
Then humans start showing up all over Ponyville, as well, pony's start disappearing. The chaos is ensuing as Twilight and Fluttershy engage Discord believing him to be responsible. While he's having all kinds of fun over it, he is rather concerned as he's been feeling rather under the weather. Seems something has been using his power, unable to control it as everything was going crazy..
Soon much larger gaps begin to appear as whole sections of the school and Pony world begin to come together when Twilight goes to check on her human counterpart. She is reading an odd book as she reveals a book about the two worlds coming together, pony's and humans of the past using the mirror as an artifact to keep the worlds from falling apart. They go to engage (Human) Discord and plead with him to stop this but he tells them that even if he wanted to, there would be no way for him to. His power merely act as the conduit to crack the mirror, the mirror is too powerful for him to fix.
The Human Discord, was also feeling rather sick as Pony Discord explains that his power is linked to Pony World, and with both worlds coming together, all of pony world magic would vanish with it. Human discord didn't want to hurt pony world, he revealed his intentions were never to hurt anyone, he wanted to share the worlds with the other, two worlds becoming one utopia for both kinds. He shows Twilight where the mirror was as pony and human twilight both try to fix the mirror with the spell, being unable to they consult Celestia, as all the ponies were starting to look sickly as their powers faded. Twilights friends (pony and human) show up as they all seemed determined to help.
In one last effort they use the power of friendship to try and fix it, as the pony's activate the power, the humans gain their pony features as they all float up, their powers of friendship activating and fixing the mirror between the human and pony world. All the humans start going back through the portal, saying goodbye to their pony counter part. Twilights friends all wish they could hang out longer, but realize they have to say good bye.
Just a thought.... it's imperfect cause in the middle I would love to see a scene where Human rarity takes pony rarity into her clothes shop as they make designs together. Pony and human dash play soccer, Twilights trade books, Human Fluttershy shows Pony fluttershy the animals at her donation center, Human Appledash working on the apple farm. Human and pony pinky work together to set up something really big and exciting as they reveal at the end they were working on a good bye party as they knew they'd have to say goodbye.
hope you like the idea anyway.