Notice: The Crossover Tag is just to be on the safe side
After Twilight Sparkle convinced Starlight Glimmer to let the Rainboom happen and returning to the proper timeline, the time vortex mysteriously didn't close after swallowing up Starlight's modified spell, and what's more, more time vortexes were popping up all over Canterlot and Ponyville alike; one even popping up in the everfree forest itself as the earth itself began to shake.
Meanwhile, in the far-off future Sunny Starscout had gathered her friends, Sprout, and the leaders of the respective races to try and figure out the secrets of the merged crystal. While running tests, the crystal suddenly went critical and sucked all of the ponies across the globe into mysterious portals.
Things are about to get hectic for both sides as the two generations will suddenly find out what happens when their times collide.