It's been almost two years since the Order-naries left Equestria to return to their own universe, and the world has moved on without them. Twilight, now an alicorn princess of Equestria, continues to live in Ponyville and tries to carry on a normal life in between her self-guided research into new magic and the occasional problems in the neighborhood. As she has done from time to time over the past couple of years, she has started to search for a way to see the world of the Order-naries as a prelude to reestablishing contact with them.
After a fruitless attempt to scry across the dimensions, a strange sequence of events takes place that gives Twilight a bad case of deja vu: a dimensional portal tears open near Fluttershy's house, a large magical gemstone crashes into Rarity's house, and three familiar-looking ponies appear and plunge deep into the Everfree Forest without a word to anypony.
Mysteries abound, and nopony seems to have an answer.